fix(action): allow forward sync from trailer commits

# Conflicts:
#	CHANGELOG.md

.gitignore

@@ -1,3 +1,4 @@
 .claude/*local*
-
+dist/
+.env
 result

CHANGELOG.md

@@ -1,5 +1,187 @@
 # Changelog
 
+## 2.2.2
+
+### Fixes
+
+- Forward sync no longer skips the entire action when the checked-out HEAD commit has the configured sync trailer. This allows valid multi-hop setups where one repo receives sync commits from an upstream repository and forwards its filtered subtree to another repository. Reverse sync still filters bot commits by trailer for loop prevention.
+
+## 2.2.1
+
+### Fixes
+
+- Initial import now force-adds copied subrepo files so tracked files that match the copied `.gitignore` are included in the import PR.
+
+## 2.2.0
+
+### Changes
+
+- **Unified onboarding via `josh-sync onboard <target>`.** The previously separate `adopt` workflow is now an onboarding strategy alongside the original `reset` flow. Strategy is resolved by precedence: `--mode={reset,adopt}` flag → `targets[].history_lock` config (`preserve` → adopt, `rewrite` → reset) → auto-detect via `git ls-remote --heads` on the subrepo (heads → adopt, empty → reset). The chosen strategy is logged at preflight (and re-announced on every resume).
+- **`josh-sync adopt` kept as a back-compat CLI alias** for `josh-sync onboard --mode=adopt`. Existing in-flight adoptions (state at `<target>/adopt.json` on the `josh-sync-state` branch) continue to resume — `read_onboard_state` falls back to that legacy file with an implicit `strategy: adopt` and strips the legacy `.mode` field. Pre-unification `onboard.json` files (no `.strategy`) are read as `strategy: reset`.
+- **New `targets[].history_lock` config field** (`preserve` | `rewrite`) — pins the onboarding strategy independently of the subrepo's current emptiness. Validated at config parse time. See [Config Reference](docs/config-reference.md#targets-section).
+- **End-to-end bats coverage** — tree-mismatch surfacing, idempotency, merge shape (ADR-005 trailer, ADR-008 first-parent ordering), fast-forward push semantics, reverse-sync loop guard, linearize-fallback selection, resume from every checkpoint, strategy resolution precedence, legacy-state migration, and the CLI surface (flag parsing, alias forwarding, error messages).
+
+### Safety
+
+- **Auto-detect now distinguishes auth/network failures from genuinely empty repos.** A failing `git ls-remote` previously fell through to `reset` (destructive force-push); it now dies with a clear "pass --mode explicitly" message.
+- **Resume validates `--mode` against the strategy already saved in state.** Conflicting flags die with a `--restart` hint instead of being silently ignored.
+- **`josh-sync adopt` rejects a conflicting `--mode`.** Previously the user-supplied flag silently won.
+- **Missing import-PR lookup now `die`s in both strategies.** The reset path used to `WARN` and continue without recording the PR number, leading to duplicate import PRs on resume.
+- **`--restart` durably removes the legacy `<target>/adopt.json`** from the state branch so it can't silently resurrect via the read fallback.
+- **`adopt_branch` is now a subshell function** — its EXIT trap can no longer clobber callers' traps (test reporting, etc.).
+- **Strategy value is validated** after resolve/load (`reset|adopt`); unknown/corrupt values die with a `--restart` hint.
+- **`--mode` with a missing/empty value** dies with a usage hint instead of crashing under `set -u`.
+- **`migrate-pr` against an adopt-strategy target** dies with a specific message rather than the misleading "Run onboard first" loop.
+- **Reset import step asserts `archived_url` is present** instead of silently flowing the literal string `"null"` into `git clone`.
+
+ADR-013 updated with a status note pointing at the unified command.
+
+### Fixes
+
+- Makefile `dist/josh-sync` bundle header now correctly interpolates VERSION and line count (was emitting empty values due to make's `$(...)` swallowing the shell command substitution).
+
+## 2.1.0
+
+### Breaking Changes
+
+_None._
+
+### Features
+
+- **`adopt` command for non-destructive existing subrepos**: `josh-sync adopt <target>` imports existing subrepo content into the monorepo, waits for the import PR to merge, then creates an adoption merge commit on the subrepo. The adoption merge uses the Josh-filtered monorepo commit as first parent and the existing subrepo commit as second parent, preserving old subrepo history while establishing Josh-compatible ancestry.
+- **Resumable adoption state**: adoption progress is stored on `josh-sync-state` at `<target>/adopt.json`, separate from sync and onboard state.
+
+### Safety
+
+- Adoption requires the subrepo tree to match the Josh-filtered monorepo tree before creating the merge commit.
+- Adoption pushes with a normal fast-forward push only. It never force-pushes.
+
+## 2.0.0
+
+### Breaking Changes
+
+- **`schema_version: 2` is now required.** v1 configs are rejected with a migration pointer. Add `schema_version: 2` at the top of `.josh-sync.yml`.
+- **`josh.monorepo_url` is now required.** Set it to your monorepo's git clone URL — `git@host:org/repo.git` (SSH), `ssh://...`, or `https://host/org/repo.git`. Removes the silent inference of the gitea host from the first target's `subrepo_url`, which silently misbehaved when the monorepo and a target lived on different gitea instances. See [ADR-012](docs/adr/012-explicit-monorepo-url.md).
+- **`MONOREPO_API` derivation changed.** The default is now `https://{monorepo_url's host}/api/v1/repos/{monorepo_path}`. The env-var override is preserved as an escape hatch for custom API endpoints.
+
+#### Migration
+
+```yaml
+# Before (v1.x)
+josh:
+  proxy_url: "https://josh.example.com"
+  monorepo_path: "org/monorepo"
+
+# After (v2.0.0)
+schema_version: 2
+josh:
+  proxy_url: "https://josh.example.com"
+  monorepo_path: "org/monorepo"
+  monorepo_url: "git@gitea.example.com:org/monorepo.git"   # required
+  monorepo_auth: "ssh"                                       # optional, default "https"
+```
+
+If you previously set the `MONOREPO_API` env var to work around the first-target-host bug, you can remove it — the new derivation gets it right from `monorepo_url`.
+
+### Features
+
+- **Multi-host configs supported.** The monorepo and any subrepo may live on different gitea instances. Target ordering no longer affects how the monorepo's host is resolved.
+- **SSH clone of the monorepo via `monorepo_auth: ssh`.** Uses the user's ssh-agent / `~/.ssh/config`; no token required for the clone itself. PR creation still uses `GITEA_TOKEN`.
+- **Symmetric config shape.** Monorepo and subrepos now both declare a URL plus an auth method.
+
+### Fixes
+
+- First-target ordering no longer load-bearing on `MONOREPO_API` derivation (was `gitea_host=.[0].gitea_host` in v1.x).
+
+## 1.5.0
+
+### Breaking Changes
+
+_None._
+
+### Features
+
+- **`--force` flag for reverse sync**: `josh-sync sync --reverse --force` bypasses
+  the PR step and force-pushes the subrepo's state directly onto the monorepo branch.
+  Also skips the `skip-dirty` guard. Only valid with `--reverse`. Returns status `forced`.
+
+## 1.4.0
+
+### Breaking Changes
+
+_None._
+
+### Features
+
+- **`schema_version` config field**: New optional integer field in `.josh-sync.yml`. Defaults to `1` when absent. josh-sync fails fast with a clear error if an unsupported version is present — safe path for future config migrations without silent misinterpretation.
+
+### Fixes
+
+- **Linearize fallback applying wrong diff**: Fallback for failed `cherry-pick` was diffing from `HEAD` to the commit's full tree instead of from the commit's own parent, causing unrelated file deletions. Now diffs from the commit's own parent (`${sha}^` / `${sha}^1`).
+- **Linearize fallback for already-applied merge commits**: When `cherry-pick -m 1` produces an empty result because a merge's changes were already applied by a prior cherry-pick, the commit is now skipped instead of attempting a failing `git apply`.
+- **Linearize fallback output**: Suppressed git noise from cherry-pick, checkout, and commit during linearization; added delimiters and consistent indented log lines.
+
+### Docs
+
+- Workflow guide: removed redundant step-by-step subsections (table already covers them); tightened ADR-011 alternatives; removed stale version pins.
+- README: added Versioning section with semver policy table and floating tag explanation.
+
+## 1.3.0
+
+### Breaking Changes
+
+_None._
+
+### Features
+
+- **Linearize fallback for reverse sync**: When josh-proxy rejects a push due to unmappable merge commits, reverse sync automatically falls back to linearizing the history — cherry-picking regular commits individually and squashing only the problematic merge commits via `cherry-pick -m 1`. Preserves individual commit granularity while handling complex merge topologies that josh cannot map. PR body notes when linearization was used.
+
+### Fixes
+
+- **Reverse sync human commit detection**: Fixed `--ancestry-path` returning empty when `mono-filtered` has advanced past the last forward sync. Any monorepo commit (even outside the subfolder) causes josh to create a new filtered commit, breaking the ancestry path to subrepo HEAD. Now uses `git merge-base` to find the last connected point.
+- **State not updated on false skip**: When trees differ but no human commits are found, reverse sync now returns `skip-dirty` instead of `skip`. State is not updated, so the system retries on the next run instead of silently dropping commits.
+
+### Docs
+
+- Expanded troubleshooting guide for "Josh rejected push" with root cause analysis and prevention advice.
+- Added ADR-011: Linearize fallback for reverse sync.
+- Added recommended Git workflow section to the guide.
+
+## 1.2.0
+
+### Breaking Changes
+
+_None._
+
+### Features
+
+- **File exclusion**: `exclude` config field removes files/directories from the subrepo at the josh-proxy transport layer. Patterns are embedded inline in the josh-proxy URL using `:exclude[::pattern,...]` syntax — no extra files to generate or commit.
+- **Filter change reconciliation**: When the josh filter changes (e.g., adding/removing exclude patterns), josh-sync automatically creates a reconciliation merge commit that connects old and new histories. No manual reset or force-push required.
+- **Tree comparison guard**: Reverse sync now compares subrepo tree to josh-filtered tree before checking commit log. Skips immediately when trees are identical, avoiding false positives from reconciliation merge history.
+- **Unrelated histories detection**: Forward sync detects when histories are unrelated (no common ancestor) and falls back to reconciliation instead of creating a useless conflict PR.
+
+### Fixes
+
+- Pre-v1.2 state compatibility: When upgrading from v1.0/v1.1 (no `josh_filter` stored in state), the old filter is derived from `subfolder` so reconciliation triggers correctly.
+- Reconciliation merge parent order: Josh-filtered history is always first parent so josh-proxy can follow first-parent traversal back to the monorepo.
+- Reverse sync `--ancestry-path` flag prevents old subrepo history from leaking through reconciliation merge parents.
+- PR body `\n` now renders as actual newlines instead of literal text.
+- Conflict result no longer updates sync state (added `continue` to skip state write).
+- `action.yml` now copies VERSION file for correct `--version` output in CI.
+- `.gitignore` now includes `dist/` and `.env`.
+
+## 1.1.0
+
+### Breaking Changes
+
+_None._
+
+### Features
+
+- **`onboard` command**: Interactive, resumable workflow for importing existing subrepos into the monorepo. Walks through: prerequisites check, import (creates PRs), wait for merge, reset (pushes josh-filtered history). Checkpoint/resume at every step.
+- **`migrate-pr` command**: Migrates open PRs from an archived subrepo to the new one. Supports interactive selection, `--all` flag, and specific PR numbers. Uses `git apply --3way` for resilient patch application.
+- **Onboard state tracking**: Stored on the `josh-sync-state` branch at `<target>/onboard.json`. Tracks step progress, import PR numbers, reset branches, and migrated PRs.
+
 ## 1.0.0
 
 Initial release. Extracted from [private-monorepo-example](https://code.itkan.io/pe/private-monorepo-example) into a standalone reusable library.

Makefile

@@ -19,11 +19,11 @@ dist/josh-sync: bin/josh-sync lib/*.sh VERSION
 	@mkdir -p dist
 	@echo "Bundling josh-sync..."
 	@echo '#!/usr/bin/env bash' > dist/josh-sync
-	@echo "# josh-sync $(cat VERSION) — bundled distribution" >> dist/josh-sync
+	@echo "# josh-sync $$(cat VERSION) — bundled distribution" >> dist/josh-sync
 	@echo '# Generated by: make build' >> dist/josh-sync
 	@echo '' >> dist/josh-sync
 	@# Inline all library modules (strip shebangs and source directives)
-	@for f in lib/core.sh lib/config.sh lib/auth.sh lib/state.sh lib/sync.sh lib/onboard.sh; do \
+	@for f in lib/core.sh lib/config.sh lib/auth.sh lib/state.sh lib/sync.sh lib/adopt.sh lib/onboard.sh; do \
 		echo "# --- $$f ---" >> dist/josh-sync; \
 		grep -v '^#!/' "$$f" | grep -v '^# shellcheck source=' >> dist/josh-sync; \
 		echo '' >> dist/josh-sync; \
@@ -36,7 +36,7 @@ dist/josh-sync: bin/josh-sync lib/*.sh VERSION
 		| sed '/^JOSH_LIB_DIR=/,/^source/d' \
 		>> dist/josh-sync
 	@chmod +x dist/josh-sync
-	@echo "Built: dist/josh-sync ($(wc -l < dist/josh-sync) lines)"
+	@echo "Built: dist/josh-sync ($$(wc -l < dist/josh-sync) lines)"
 
 clean:
 	rm -rf dist/

README.md

@@ -9,19 +9,23 @@ Bidirectional monorepo ↔ subrepo sync via [josh-proxy](https://josh-project.gi
 Create `.josh-sync.yml` in your monorepo root:
 
 ```yaml
+schema_version: 2
+
 josh:
   proxy_url: "https://josh.example.com"
   monorepo_path: "org/monorepo"
+  monorepo_url: "git@gitea.example.com:org/monorepo.git"
+  monorepo_auth: "ssh"               # optional, default "https"
 
 targets:
   - name: "billing"
     subfolder: "services/billing"
-    josh_filter: ":/services/billing"
     subrepo_url: "git@gitea.example.com:ext/billing.git"
     subrepo_auth: "ssh"
     branches:
       main: main
-    forward_only: []
+    exclude:                          # files excluded from subrepo (optional)
+      - ".monorepo/"
 
 bot:
   name: "josh-sync-bot"
@@ -58,15 +62,30 @@ Run `josh-sync preflight` to validate your setup.
 
 ## Documentation
 
-- **[Setup Guide](docs/guide.md)** — Step-by-step: prerequisites, importing existing subrepos, CI workflows, and troubleshooting
+- **[Setup Guide](docs/guide.md)** — Step-by-step: prerequisites, importing existing subrepos, CI workflows, file exclusion, and troubleshooting
 - **[Configuration Reference](docs/config-reference.md)** — Full `.josh-sync.yml` field documentation
+- **[Architecture Decision Records](docs/adr/)** — Design rationale and trade-offs
+- **[Changelog](CHANGELOG.md)** — Version history
+
+## Versioning
+
+josh-sync follows [semver](https://semver.org/):
+
+| Bump | Meaning | Action required |
+|------|---------|-----------------|
+| **Patch** (1.x.**y**) | Bug fixes only | Safe to upgrade |
+| **Minor** (1.**y**.0) | New optional config fields, new commands, new action inputs | Safe to upgrade; new features are opt-in |
+| **Major** (**y**.0.0) | Removed or renamed config fields, CLI flags, action inputs, env vars, or state format | Read the **Breaking Changes** section in the changelog before upgrading |
+
+CI workflows pin to a floating major tag (e.g. `@v1`). A breaking change bumps the major version and moves the tag — `@v1` workflows keep working until you explicitly update to `@v2`.
 
 ## CLI
 
 ```
-josh-sync sync [--forward|--reverse] [--target NAME[,NAME]] [--branch BRANCH]
+josh-sync sync [--forward|--reverse] [--force] [--target NAME[,NAME]] [--branch BRANCH]
 josh-sync preflight
 josh-sync import <target>
+josh-sync adopt <target> [--restart]
 josh-sync reset <target>
 josh-sync onboard <target> [--restart]
 josh-sync migrate-pr <target> [PR#...] [--all]
@@ -78,13 +97,18 @@ josh-sync state reset <target> [branch]
 ## How It Works
 
 - **Forward sync** (mono → subrepo): pushes directly if clean, creates conflict PR if not. Uses `--force-with-lease` for safety.
-- **Reverse sync** (subrepo → mono): always creates a PR, never pushes directly.
+- **Reverse sync** (subrepo → mono): creates a PR by default. Add `--force` to bypass the PR and push directly to the mono branch (destructive).
+- **Adoption**: existing active subrepos can be connected to josh-sync with a normal fast-forward merge commit, preserving old subrepo history and avoiding force-push.
+- **File exclusion**: `exclude` patterns are embedded inline in the josh-proxy URL. Excluded files exist only in the monorepo.
+- **Filter reconciliation**: Changing the exclude list auto-creates a merge commit that connects old and new histories — no force-push needed.
 - **Loop prevention**: `Josh-Sync-Origin:` git trailer filters out bot commits.
 - **State tracking**: orphan branch `josh-sync-state` stores JSON per target/branch.
 
 ## Dependencies
 
-`bash >=4`, `git`, `curl`, `jq`, `yq` ([mikefarah/yq](https://github.com/mikefarah/yq) v4+), `openssh`
+`bash >=4`, `git`, `curl`, `jq`, `yq` ([mikefarah/yq](https://github.com/mikefarah/yq) v4+), `openssh`, `rsync`
+
+> The Nix flake bundles all dependencies automatically.
 
 ## License
 

VERSION

@@ -1 +1 @@
-1.1.0
+2.2.2

action.yml

@@ -26,6 +26,7 @@ runs:
       run: |
         JOSH_DIR="$(mktemp -d)"
         cp -r "${{ github.action_path }}/bin" "${{ github.action_path }}/lib" "${JOSH_DIR}/"
+        cp "${{ github.action_path }}/VERSION" "${JOSH_DIR}/" 2>/dev/null || true
         chmod +x "${JOSH_DIR}/bin/josh-sync"
         echo "${JOSH_DIR}/bin" >> "$GITHUB_PATH"
         echo "JOSH_SYNC_ROOT=${JOSH_DIR}" >> "$GITHUB_ENV"
@@ -37,21 +38,7 @@ runs:
           command -v "$cmd" &>/dev/null || { echo "::error::Missing required tool: $cmd"; exit 1; }
         done
 
-    - name: Loop guard (forward)
-      id: guard
-      if: inputs.direction == 'forward' || inputs.direction == 'both'
-      shell: bash
-      run: |
-        TRAILER=$(yq '.bot.trailer' "${{ inputs.config }}" 2>/dev/null || echo "Josh-Sync-Origin")
-        if git log -1 --format=%B | grep -q "^${TRAILER}:"; then
-          echo "skip=true" >> "$GITHUB_OUTPUT"
-          echo "::notice::Skipping sync — HEAD commit has sync trailer (loop prevention)"
-        else
-          echo "skip=false" >> "$GITHUB_OUTPUT"
-        fi
-
     - name: Sync
-      if: steps.guard.outputs.skip != 'true'
       shell: bash
       env:
         JOSH_SYNC_DEBUG: ${{ inputs.debug == 'true' && '1' || '0' }}

bin/josh-sync

@@ -8,8 +8,9 @@
 #   sync              Run forward and/or reverse sync
 #   preflight         Validate config, connectivity, auth
 #   import <target>   Initial import: pull subrepo into monorepo
+#   onboard <target>  Interactive onboarding (auto-picks reset|adopt strategy)
+#   adopt <target>    Alias for `onboard --mode=adopt`
 #   reset <target>    Reset subrepo to josh-filtered view
-#   onboard <target>  Import existing subrepo into monorepo (interactive)
 #   migrate-pr <target> [PR#...] [--all]   Move PRs from archived to new subrepo
 #   status            Show target config and sync state
 #   state show|reset  Manage sync state directly
@@ -41,6 +42,8 @@ source "${JOSH_LIB_DIR}/auth.sh"
 source "${JOSH_LIB_DIR}/state.sh"
 # shellcheck source=../lib/sync.sh
 source "${JOSH_LIB_DIR}/sync.sh"
+# shellcheck source=../lib/adopt.sh
+source "${JOSH_LIB_DIR}/adopt.sh"
 # shellcheck source=../lib/onboard.sh
 source "${JOSH_LIB_DIR}/onboard.sh"
 
@@ -72,8 +75,13 @@ Commands:
   sync              Run forward and/or reverse sync
   preflight         Validate config, connectivity, auth, workflow coverage
   import <target>   Initial import: pull existing subrepo into monorepo (creates PR)
+  onboard <target>  Onboard a subrepo (interactive, resumable). Picks a strategy:
+                      reset  — force-push josh-filtered history (replaces subrepo)
+                      adopt  — non-destructive merge that keeps subrepo history
+                    Precedence: --mode flag > targets[].history_lock > auto-detect
+                    via ls-remote (heads → adopt, empty → reset).
+  adopt <target>    Alias for 'onboard --mode=adopt' (kept for back-compat)
   reset <target>    Reset subrepo to josh-filtered view (after merging import PR)
-  onboard <target>  Import existing subrepo into monorepo (interactive, resumable)
   migrate-pr <target> [PR#...] [--all]  Move PRs from archived to new subrepo
   status            Show target config and sync state
   state show <target> [branch]    Show sync state JSON
@@ -88,9 +96,13 @@ Global flags:
 Sync flags:
   --forward         Forward only (mono → subrepo)
   --reverse         Reverse only (subrepo → mono)
+  --force           Force-push subrepo state to mono branch (--reverse only, skips PR)
   --target NAME     Filter to target(s) — comma-separated for multiple (env: JOSH_SYNC_TARGET)
   --branch BRANCH   Filter to one branch
 
+Onboard flags:
+  --mode={reset,adopt}  Override the onboarding strategy
+
 Environment:
   JOSH_SYNC_TARGET       Restrict to a single target name
   JOSH_SYNC_STATE_BRANCH State branch name (default: josh-sync-state)
@@ -108,6 +120,7 @@ cmd_sync() {
   local filter_target="${JOSH_SYNC_TARGET:-}"
   local filter_branch=""
   local config_file=".josh-sync.yml"
+  local force_flag=false
 
   while [ $# -gt 0 ]; do
     case "$1" in
@@ -117,10 +130,18 @@ cmd_sync() {
       --branch)  filter_branch="$2"; shift 2 ;;
       --config)  config_file="$2"; shift 2 ;;
       --debug)   export JOSH_SYNC_DEBUG=1; shift ;;
+      --force)   force_flag=true; shift ;;
       *) die "Unknown flag: $1" ;;
     esac
   done
 
+  if [ "$force_flag" = true ] && [ "$direction" != "reverse" ]; then
+    die "--force requires --reverse"
+  fi
+  if [ "$force_flag" = true ]; then
+    export SYNC_REVERSE_FORCE=1
+  fi
+
   parse_config "$config_file"
 
   # Forward sync
@@ -208,13 +229,42 @@ _sync_direction() {
         fi
       fi
 
-      # Run sync
+      # Check for filter change (forward only — reverse uses same filter)
       local result
       if [ "$direction" = "forward" ]; then
+        local prev_filter
+        prev_filter=$(echo "$state" | jq -r '.last_forward.josh_filter // empty')
+
+        # If no filter stored (pre-v1.2 state) but a previous sync exists,
+        # the old filter was the simple :/subfolder (before exclude was added)
+        if [ -z "$prev_filter" ]; then
+          local prev_mono_sha
+          prev_mono_sha=$(echo "$state" | jq -r '.last_forward.mono_sha // empty')
+          if [ -n "$prev_mono_sha" ]; then
+            local subfolder
+            subfolder=$(echo "$TARGET_JSON" | jq -r '.subfolder')
+            prev_filter=":/${subfolder}"
+          fi
+        fi
+
+        if [ -n "$prev_filter" ] && [ "$prev_filter" != "$JOSH_FILTER" ]; then
+          log "WARN" "Josh filter changed — reconciling histories"
+          log "INFO" "Old: ${prev_filter}"
+          log "INFO" "New: ${JOSH_FILTER}"
+          result=$(reconcile_filter_change)
+        else
           result=$(forward_sync)
+        fi
       else
         result=$(reverse_sync)
       fi
+      # If forward sync hit unrelated histories, fall back to reconciliation
+      if [ "$result" = "unrelated" ]; then
+        log "WARN" "Unrelated histories detected — falling back to filter reconciliation"
+        result=$(reconcile_filter_change)
+        log "INFO" "Reconciliation result: ${result}"
+      fi
+
       log "INFO" "Result: ${result}"
 
       # Handle warnings
@@ -224,11 +274,19 @@ _sync_direction() {
       fi
       if [ "$result" = "conflict" ]; then
         echo "::warning::Target ${target_name}, branch ${branch}: merge conflict — PR created on subrepo"
+        continue
       fi
       if [ "$result" = "josh-rejected" ]; then
         echo "::error::Target ${target_name}, branch ${branch}: josh rejected push — check proxy logs"
         continue
       fi
+      if [ "$result" = "skip-dirty" ]; then
+        log "WARN" "Trees differ but no human commits — skipping state update (will retry)"
+        continue
+      fi
+      if [ "$result" = "forced" ]; then
+        log "WARN" "Target ${target_name}, branch ${branch}: force-pushed subrepo directly to mono — DESTRUCTIVE"
+      fi
 
       # Update state (only on success)
       local new_state
@@ -240,8 +298,9 @@ _sync_direction() {
           --arg s_sha "${subrepo_sha_now:-}" \
           --arg ts "$(date -u +%Y-%m-%dT%H:%M:%SZ)" \
           --arg status "$result" \
+          --arg filter "$JOSH_FILTER" \
           --argjson prev "$state" \
-          '$prev + {last_forward: {mono_sha:$m_sha, subrepo_sha:$s_sha, timestamp:$ts, status:$status}}')
+          '$prev + {last_forward: {mono_sha:$m_sha, subrepo_sha:$s_sha, timestamp:$ts, status:$status, josh_filter:$filter}}')
       else
         local mono_sha_now
         mono_sha_now=$(git rev-parse "origin/${branch}" 2>/dev/null || echo "")
@@ -482,6 +541,35 @@ cmd_import() {
   done
 }
 
+# ─── Adopt Command (alias) ─────────────────────────────────────────
+# `josh-sync adopt` is preserved as a thin alias for the unified onboard
+# command. Effectively: `josh-sync onboard --mode=adopt <args...>`.
+
+cmd_adopt() {
+  # Reject a conflicting --mode in the forwarded args: the alias means adopt,
+  # so `josh-sync adopt … --mode=reset` is contradictory. Without this guard
+  # the user-supplied --mode would silently win (last --mode in cmd_onboard's
+  # parser is the one that takes effect).
+  local i=1 a
+  while [ $i -le $# ]; do
+    a="${!i}"
+    case "$a" in
+      --mode=adopt) ;;
+      --mode=*) die "'josh-sync adopt' is an alias for --mode=adopt; conflicting '${a}' given. Use 'josh-sync onboard <target>' instead." ;;
+      --mode)
+        i=$((i + 1))
+        if [ $i -gt $# ] || [ "${!i}" != "adopt" ]; then
+          die "'josh-sync adopt' is an alias for --mode=adopt; conflicting '--mode ${!i:-<missing>}' given. Use 'josh-sync onboard <target>' instead."
+        fi
+        ;;
+    esac
+    i=$((i + 1))
+  done
+
+  log "INFO" "(josh-sync adopt is now an alias for: josh-sync onboard --mode=adopt)"
+  cmd_onboard --mode=adopt "$@"
+}
+
 # ─── Reset Command ─────────────────────────────────────────────────
 
 cmd_reset() {
@@ -655,19 +743,25 @@ cmd_onboard() {
   local config_file=".josh-sync.yml"
   local target_name=""
   local restart=false
+  local mode=""
 
   while [ $# -gt 0 ]; do
     case "$1" in
       --config)   config_file="$2"; shift 2 ;;
       --debug)    export JOSH_SYNC_DEBUG=1; shift ;;
       --restart)  restart=true; shift ;;
+      --mode=*)   mode="${1#--mode=}"
+                  [ -n "$mode" ] || die "Empty --mode= (use --mode=reset|adopt)"
+                  shift ;;
+      --mode)     [ $# -ge 2 ] || die "--mode requires a value (reset|adopt)"
+                  mode="$2"; shift 2 ;;
       -*) die "Unknown flag: $1" ;;
       *)  target_name="$1"; shift ;;
     esac
   done
 
   if [ -z "$target_name" ]; then
-    echo "Usage: josh-sync onboard <target> [--restart]" >&2
+    echo "Usage: josh-sync onboard <target> [--mode=reset|adopt] [--restart]" >&2
     parse_config "$config_file"
     echo "Available targets:" >&2
     echo "$JOSH_SYNC_TARGETS" | jq -r '.[].name' | sed 's/^/  /' >&2
@@ -682,7 +776,7 @@ cmd_onboard() {
 
   log "INFO" "══════ Onboard target: ${target_name} ══════"
   load_target "$target_json"
-  onboard_flow "$target_json" "$restart"
+  onboard_flow "$target_json" "$restart" "$mode"
 }
 
 # ─── Migrate PR Command ──────────────────────────────────────────
@@ -838,6 +932,7 @@ main() {
     sync)       cmd_sync "$@" ;;
     preflight)  cmd_preflight "$@" ;;
     import)     cmd_import "$@" ;;
+    adopt)      cmd_adopt "$@" ;;
     reset)      cmd_reset "$@" ;;
     onboard)    cmd_onboard "$@" ;;
     migrate-pr) cmd_migrate_pr "$@" ;;

docs/adr/001-josh-proxy-for-sync.md

@@ -0,0 +1,42 @@
+# ADR-001: Josh-proxy for Bidirectional Sync
+
+**Status:** Accepted
+**Date:** 2026-01
+
+## Context
+
+We need bidirectional sync between a monorepo and N external subrepos. Each subrepo corresponds to a subfolder in the monorepo. Developers on both sides should see a clean, complete git history — not synthetic commits or squashed blobs.
+
+### Alternatives considered
+
+1. **git subtree**: Built into git. `git subtree split` extracts a subfolder into a standalone repo. However, subtree split rewrites history on every run (O(n) on total commits), creating new SHAs each time. Bidirectional sync requires manual `subtree merge` with conflict-prone history grafting. No transport-layer filtering — all content must be fetched.
+
+2. **git submodule**: Tracks external repos via `.gitmodules` pointer commits. Does not provide content-level integration — monorepo commits don't contain subrepo files directly. Developers must run `git submodule update`. Bidirectional sync is not a supported workflow.
+
+3. **Custom diff-and-patch scripts**: Compute diffs between monorepo subfolder and subrepo, apply patches in both directions. Fragile with renames, binary files, and merge conflicts. Loses authorship and commit granularity.
+
+4. **josh-proxy**: A git proxy that computes filtered views of repositories in real-time. Clients `git clone` through josh and receive a repo containing only the specified subfolder, with history rewritten to match. Josh maintains a persistent SHA mapping, so the same monorepo commit always produces the same filtered SHA. Bidirectional: pushing back through josh maps filtered commits to monorepo commits.
+
+## Decision
+
+Use josh-proxy as the transport layer for all sync operations.
+
+## Consequences
+
+**Positive:**
+- Clean git history in both directions — no synthetic commits
+- Deterministic SHA mapping — same monorepo state always produces same filtered SHA
+- Bidirectional by design — push through josh maps back to monorepo
+- Transport-layer filtering — content exclusion happens at clone/push time, not via generated files
+- Supports any git hosting platform (Gitea, GitHub, GitLab) since it's a proxy
+
+**Negative:**
+- Requires running a josh-proxy instance (operational overhead)
+- Josh-proxy is a Rust project with a smaller community than git-native tools
+- Proxy must have network access to the monorepo's git server
+- Josh's SHA mapping is opaque — debugging requires understanding josh internals
+- First-parent traversal behavior must be respected in merge commits (see ADR-008)
+
+**Risks:**
+- Josh-proxy downtime blocks all sync operations
+- Josh-proxy bugs could corrupt history mapping (mitigated by force-with-lease on forward, always-PR on reverse)

docs/adr/002-state-on-orphan-branch.md

@@ -0,0 +1,50 @@
+# ADR-002: State Storage on Orphan Git Branch
+
+**Status:** Accepted
+**Date:** 2026-01
+
+## Context
+
+Josh-sync needs persistent state to track what has already been synced (last-synced commit SHAs, timestamps, status). This prevents re-syncing unchanged content and enables incremental operation. The state must survive CI runner teardown — runners are ephemeral containers.
+
+### Alternatives considered
+
+1. **File in the repo**: Commit a state JSON file to the monorepo. Every sync run creates a commit, polluting history. Race conditions when multiple sync jobs run concurrently.
+
+2. **External database/KV store**: Redis, SQLite, or a cloud KV service. Adds an infrastructure dependency. Credentials and connectivity to manage.
+
+3. **CI artifacts/cache**: Platform-specific (GitHub Actions cache, Gitea cache). Not portable across CI platforms. Expiry policies vary.
+
+4. **Orphan git branch**: A branch with no parent relationship to the main history. Stores JSON files in a simple `<target>/<branch>.json` layout. Pushed to origin, so it survives runner teardown. No external dependencies — uses git itself.
+
+## Decision
+
+Store sync state as JSON files on an orphan branch (`josh-sync-state`) in the monorepo.
+
+### Storage layout
+
+```
+origin/josh-sync-state/
+  <target>/<branch>.json       # sync state per target/branch
+  <target>/onboard.json        # onboard workflow state (v1.1+)
+```
+
+### Implementation
+
+- `read_state()`: `git fetch origin josh-sync-state && git show origin/josh-sync-state:<key>.json`
+- `write_state()`: Uses `git worktree` to check out the orphan branch in a temp directory, writes JSON, commits, and pushes. This avoids touching the main working tree.
+
+## Consequences
+
+**Positive:**
+- Zero external dependencies — only git
+- Portable across CI platforms (Gitea Actions, GitHub Actions, local)
+- Human-readable JSON files — easy to inspect and debug
+- Atomic updates via git commit + push
+- Natural namespacing via directory structure
+
+**Negative:**
+- Concurrent writes can race (mitigated by concurrency groups in CI workflows)
+- `git worktree` adds complexity to the write path
+- State branch appears in `git branch -a` output (minor clutter)
+- Push failures on the state branch are non-fatal (logged as warning, sync still succeeds)

docs/adr/003-force-with-lease-forward.md

@@ -0,0 +1,33 @@
+# ADR-003: Force-with-Lease for Forward Sync
+
+**Status:** Accepted
+**Date:** 2026-01
+
+## Context
+
+Forward sync pushes monorepo changes to the subrepo. If someone pushes directly to the subrepo between when josh-sync reads its HEAD and when josh-sync pushes, a naive `git push` would overwrite their work. A `git push --force` would be worse — it would silently destroy concurrent changes.
+
+## Decision
+
+Use `git push --force-with-lease=refs/heads/<branch>:<expected-sha>` for all forward sync pushes. The expected SHA is recorded at the start of the sync operation (the "lease").
+
+### How it works
+
+1. Record subrepo HEAD SHA before any operations: `subrepo_sha=$(subrepo_ls_remote "$branch")`
+2. Perform merge of monorepo changes onto subrepo state
+3. Push with explicit lease: `--force-with-lease=refs/heads/main:<subrepo_sha>`
+4. If the subrepo HEAD changed since step 1, git rejects the push
+5. Josh-sync reports `lease-rejected` and retries on the next run
+
+## Consequences
+
+**Positive:**
+- Never overwrites concurrent changes — git atomically checks the expected SHA
+- Explicit SHA lease (not just "current tracking ref") prevents stale-ref bugs
+- Failed leases are retried on the next sync run — no data loss, just delay
+- Works correctly with josh-proxy's SHA mapping
+
+**Negative:**
+- Lease-rejected means the sync run did work that gets discarded (clone, merge, etc.)
+- Persistent lease failures indicate a concurrent push pattern that needs investigation
+- Requires the `--force-with-lease` flag with explicit SHA — the shorthand form (`--force-with-lease` without `=`) is unsafe because it uses the local tracking ref, which may be stale

docs/adr/004-always-pr-reverse.md

@@ -0,0 +1,41 @@
+# ADR-004: Always-PR Policy for Reverse Sync
+
+**Status:** Accepted
+**Date:** 2026-01
+
+## Context
+
+Reverse sync brings subrepo changes back into the monorepo. The monorepo is the source of truth and typically has CI checks, code review requirements, and branch protection rules. Pushing directly to the monorepo's main branch would bypass these safeguards.
+
+### Alternatives considered
+
+1. **Direct push**: Fast, but bypasses all review and CI. A bad subrepo commit could break the entire monorepo with no review gate.
+
+2. **Always create a PR**: Pushes to a staging branch (`auto-sync/subrepo-<branch>-<timestamp>`), then creates a PR via API. Humans review and merge.
+
+3. **Configurable per-target**: Let users choose direct push vs PR. Adds complexity and a dangerous default.
+
+## Decision
+
+Reverse sync always creates a PR on the monorepo. Never pushes directly to the target branch.
+
+### Implementation
+
+1. Push subrepo HEAD through josh-proxy to a staging branch: `git push -o "base=main" josh://... HEAD:refs/heads/auto-sync/subrepo-main-<ts>`
+2. Create PR via Gitea/GitHub API targeting the monorepo's main branch
+3. PR includes a review checklist: scoped to subfolder, no leaked credentials, CI passes
+
+The `-o "base=main"` option tells josh-proxy which monorepo branch to map the push against.
+
+## Consequences
+
+**Positive:**
+- All monorepo changes go through review — consistent with team workflow
+- CI runs on the PR branch before merge
+- Bad subrepo changes are caught before they affect the monorepo
+- Audit trail via PR history
+
+**Negative:**
+- Reverse sync is not instant — requires human action to merge the PR
+- Stale PRs accumulate if subrepo changes frequently but PRs aren't merged promptly
+- Adds API dependency (needs token with PR creation scope)

docs/adr/005-git-trailer-loop-prevention.md

@@ -0,0 +1,52 @@
+# ADR-005: Git Trailer for Loop Prevention
+
+**Status:** Accepted
+**Date:** 2026-01
+
+## Context
+
+Bidirectional sync creates an infinite loop risk: forward sync pushes commit A to the subrepo, reverse sync sees commit A as "new" and creates a PR back to the monorepo, forward sync sees the merged PR as "new" and pushes again, etc.
+
+### Alternatives considered
+
+1. **SHA tracking only**: Compare SHAs to skip already-synced content. Breaks when josh-proxy rewrites SHAs (which it always does for filtered views). The monorepo commit SHA and the filtered/subrepo commit SHA are never the same.
+
+2. **Commit message prefix**: Add `[sync]` to bot commit messages. Fragile — humans might use the same prefix. Requires string matching on message content.
+
+3. **Git trailer**: A structured key-value pair in the commit message body (after a blank line), following the `git interpret-trailers` convention. Format: `Key: value`. Machine-parseable, unlikely to be used by humans, and supported by `git log --grep`.
+
+## Decision
+
+All bot commits include a git trailer with a configurable key (default: `Josh-Sync-Origin`). Reverse sync filters out commits containing this trailer so bot-generated forward-sync commits are not proposed back to the monorepo.
+
+### Format
+
+```
+Sync from monorepo 2026-02-12T10:30:00Z
+
+Josh-Sync-Origin: forward/main/2026-02-12T10:30:00Z
+```
+
+The trailer value encodes: direction, branch, and timestamp. This aids debugging but is not parsed by the loop filter — only the trailer key presence matters.
+
+### Filtering
+
+- **Reverse sync**: `git log --invert-grep --grep="^${BOT_TRAILER}:"` excludes all commits with the trailer
+- **Forward sync**: the composite action still runs even when HEAD has the trailer; forward sync uses tree comparison, sync state, and merge checks to decide whether to push
+
+### Configuration
+
+The trailer key is set in `.josh-sync.yml` under `bot.trailer`. This allows multiple josh-sync instances (with different bots) to operate on the same repos without interfering.
+
+## Consequences
+
+**Positive:**
+- Reliable loop prevention — trailer is part of the immutable commit object
+- Configurable key avoids conflicts between multiple sync bots
+- Human-readable — `git log` shows the trailer in commit messages
+- Repositories can act as middle hops, receiving a sync commit from one relationship and forwarding relevant changes to another
+
+**Negative:**
+- Commits with manually-added trailers matching the key would be incorrectly filtered
+- Trailer must be in the commit body (after blank line), not the subject line
+- Squash-and-merge on PRs may lose the trailer if the platform doesn't preserve commit message body

docs/adr/006-inline-exclude-filter.md

@@ -0,0 +1,55 @@
+# ADR-006: Inline Exclude in Josh-Proxy URL
+
+**Status:** Accepted
+**Date:** 2026-02
+
+## Context
+
+Some files in a monorepo subfolder should not appear in the subrepo (e.g., monorepo-specific CI configs, internal tooling, secrets templates). We need a mechanism to exclude these files from sync.
+
+### Alternatives considered
+
+1. **`.josh-sync-exclude` file committed to the repo**: A gitignore-style file listing patterns. Requires generating and committing a file. Changes to the exclude list create commits. The file itself would need to be excluded from the subrepo (circular dependency).
+
+2. **Post-clone file deletion**: Clone through josh, then `rm -rf` excluded paths before pushing. Fragile — deletions create diff noise. Doesn't work for reverse sync (excluded files would appear as "deleted" in the subrepo).
+
+3. **Josh `:exclude` filter inline in the URL**: Josh-proxy supports `:exclude[::pattern1,::pattern2]` appended to the filter path. The exclusion happens at the transport layer — git objects for excluded files are never transferred. Works identically for clone (forward) and push (reverse).
+
+4. **Separate josh filter file**: Generate a josh filter expression and store it somewhere. Adds state management complexity.
+
+## Decision
+
+Embed exclusion patterns inline in the josh-proxy URL using josh's native `:exclude` syntax. The `exclude` config field in `.josh-sync.yml` is transformed at config parse time into the josh filter string.
+
+### Example
+
+Config:
+```yaml
+exclude:
+  - ".monorepo/"
+  - "**/internal/"
+```
+
+Produces josh filter:
+```
+:/services/billing:exclude[::.monorepo/,::**/internal/]
+```
+
+### Implementation
+
+The `parse_config()` function in `lib/config.sh` uses jq to conditionally append `:exclude[...]` to the josh filter when the `exclude` array is non-empty. The enriched filter is stored in `JOSH_SYNC_TARGETS` JSON and used everywhere via `$JOSH_FILTER`.
+
+## Consequences
+
+**Positive:**
+- Zero committed files — exclusion is purely in the URL
+- Transport-layer filtering — excluded content never leaves the git server
+- Works identically for forward sync (clone), reverse sync (push), and reset
+- Tree comparison (`skip` detection) works correctly since excluded files aren't in the filtered view
+- Standard josh syntax — no custom invention
+
+**Negative:**
+- Josh's `:exclude` pattern syntax is limited (no negation, no regex — only glob-style patterns with `::` prefix)
+- Long exclude lists make the URL unwieldy (though this is cosmetic — git handles long URLs fine)
+- Changing the exclude list changes the josh filter, which changes all filtered SHAs (see ADR-007 for how this is handled)
+- Debugging requires understanding josh's filter composition syntax

docs/adr/007-reconciliation-merge.md

@@ -0,0 +1,53 @@
+# ADR-007: Reconciliation Merge for Filter Changes
+
+**Status:** Accepted
+**Date:** 2026-02
+
+## Context
+
+When the josh filter changes (e.g., adding exclude patterns), josh-proxy recomputes the entire filtered history with new SHAs. The subrepo's existing history (based on the old filter) shares no common ancestor with the new filtered history. A naive forward sync would see "unrelated histories" and fail.
+
+### Alternatives considered
+
+1. **Force-push to subrepo**: Replace subrepo history with the new filtered view (same as `josh-sync reset`). Destructive — all local clones become invalid, open PRs are orphaned, developers must re-clone.
+
+2. **Cherry-pick new commits**: Identify commits that exist in the new filtered history but not the old, cherry-pick them onto the subrepo. Complex — the "same" commit has different SHAs in old vs new filtered history. No reliable way to match them.
+
+3. **Reconciliation merge commit**: Create a merge commit on the subrepo that has both the new filtered HEAD and the old subrepo HEAD as parents, using the new filtered tree. This establishes shared ancestry without rewriting history.
+
+## Decision
+
+When josh-sync detects a filter change (stored filter in state differs from current `$JOSH_FILTER`), create a reconciliation merge commit using `git commit-tree`.
+
+### How it works
+
+1. Clone subrepo (has old history)
+2. Fetch josh-proxy filtered view (has new history)
+3. If trees are identical → skip (filter change had no effect on content)
+4. Create merge commit: `git commit-tree <josh-tree> -p <josh-head> -p <subrepo-head>`
+5. Push with `--force-with-lease`
+
+The merge commit uses the josh-filtered tree (new content) and has two parents:
+- **Parent 1**: josh-filtered HEAD (new filter history) — must be first (see ADR-008)
+- **Parent 2**: subrepo HEAD (old filter history) — preserves old history as a side branch
+
+### Detection
+
+Filter change is detected by comparing the stored `josh_filter` in sync state with the current `$JOSH_FILTER`. For pre-v1.2 state (no filter stored), the old filter is derived as `:/<subfolder>`.
+
+As a reactive fallback, `forward_sync()` also detects unrelated histories via `git merge-base` and falls back to reconciliation.
+
+## Consequences
+
+**Positive:**
+- Non-destructive — old history is preserved as parent 2 of the merge
+- Developers don't need to re-clone the subrepo
+- Open PRs on the subrepo remain valid (they're based on commits that are still ancestors)
+- Automatic — no manual intervention needed when changing exclude patterns
+- Force-with-lease protects against concurrent changes during reconciliation
+
+**Negative:**
+- The merge commit is synthetic (created by bot, not a real merge of concurrent work)
+- Parent ordering is critical — wrong order breaks josh's reverse mapping (see ADR-008)
+- The reconciliation merge contains a bot trailer, so reverse sync correctly ignores it
+- If the subrepo has diverged significantly (manual commits during filter change), the reconciliation merge may produce unexpected tree content (uses josh-filtered tree unconditionally)

docs/adr/008-first-parent-ordering.md

@@ -0,0 +1,42 @@
+# ADR-008: First-Parent Ordering in Reconciliation Merges
+
+**Status:** Accepted
+**Date:** 2026-02
+
+## Context
+
+Josh-proxy uses **first-parent traversal** when mapping subrepo history back to the monorepo. When you push a commit through josh-proxy, josh walks the first-parent chain to find a commit it can map to a monorepo commit. If the first parent leads to unmappable history, josh cannot reconstruct the monorepo-side branch correctly.
+
+This became critical when the reconciliation merge (ADR-007) initially had the wrong parent order: old subrepo history as parent 1, josh-filtered as parent 2. Josh followed parent 1, couldn't find any mappable commit, and created a monorepo branch containing only the subrepo subfolder content — effectively deleting 1280 files from the rest of the monorepo.
+
+## Decision
+
+In reconciliation merge commits, the josh-filtered HEAD **must be parent 1** (first parent). The old subrepo HEAD is parent 2.
+
+```bash
+git commit-tree "$josh_tree" \
+  -p "$josh_head" \      # parent 1: josh-filtered — josh follows this
+  -p "$subrepo_head" \   # parent 2: old history — side branch, ignored by josh
+  -m "..."
+```
+
+### Why this is safe
+
+- The old subrepo HEAD (`subrepo_head`) is still an ancestor of the merge commit regardless of parent order — push succeeds either way
+- `--ancestry-path` in reverse sync still follows `B → M → C` regardless of parent order (it traces all paths, not just first-parent)
+- Josh follows first-parent and finds the josh-filtered commit, which maps cleanly back to the monorepo
+
+## Consequences
+
+**Positive:**
+- Josh can map the reconciliation merge back to the monorepo correctly
+- Reverse sync through josh produces correct diffs (only subrepo-scoped changes)
+- `git log --first-parent` on the subrepo shows the clean josh-filtered lineage
+
+**Negative:**
+- This is a subtle invariant — future changes to merge commit creation must preserve parent order
+- The constraint is undocumented in josh-proxy's own documentation (discovered empirically)
+- No automated test can verify this without a running josh-proxy instance
+
+**Lesson learned:**
+Parent order in `git commit-tree -p` is not cosmetic. For tools that rely on first-parent traversal (josh-proxy, `git log --first-parent`), parent 1 must be the "mainline" that the tool should follow.

docs/adr/009-tree-comparison-guard.md

@@ -0,0 +1,53 @@
+# ADR-009: Tree Comparison as Sync Skip Guard
+
+**Status:** Accepted
+**Date:** 2026-02
+
+## Context
+
+Both forward and reverse sync need to detect "nothing to do" quickly. The primary mechanism is SHA comparison against stored state (last-synced SHA). However, this misses cases where:
+
+- State is reset or lost
+- Reconciliation merges change SHAs without changing content
+- Multiple sync runs overlap
+
+Additionally, reverse sync originally relied on `git log <base>..HEAD` to find new commits. After a reconciliation merge, the `..` range can leak old subrepo history through the merge's second parent, creating false positives.
+
+## Decision
+
+Add tree-level comparison as an early skip guard in both forward and reverse sync. Compare the git tree objects (which represent directory content, not commit history) to determine if there's actually any content difference.
+
+### Forward sync
+
+```bash
+mono_tree=$(git rev-parse 'HEAD^{tree}')
+subrepo_tree=$(git rev-parse "subrepo/${branch}^{tree}")
+[ "$mono_tree" = "$subrepo_tree" ] && echo "skip"
+```
+
+### Reverse sync
+
+```bash
+subrepo_tree=$(git rev-parse "HEAD^{tree}")
+josh_tree=$(git rev-parse "mono-filtered/${branch}^{tree}")
+[ "$subrepo_tree" = "$josh_tree" ] && echo "skip"
+```
+
+Tree comparison happens **before** commit log analysis. If trees are identical, there is definitionally nothing to sync, regardless of what the commit history looks like.
+
+### Combined with `--ancestry-path`
+
+For reverse sync, even when trees differ, `git log --ancestry-path` restricts the commit range to the direct lineage between the two endpoints. This prevents old history from leaking through reconciliation merge parents.
+
+## Consequences
+
+**Positive:**
+- Eliminates false positives from reconciliation merges (trees are identical after reconciliation)
+- Fast — tree SHA comparison is O(1), no content traversal
+- Correct by definition — if trees match, content is identical
+- Defense in depth — works even when state tracking has gaps
+
+**Negative:**
+- Tree comparison alone doesn't tell you *which* commits are new (still need `git log` for PR descriptions)
+- Adds an extra `git rev-parse` call per sync direction (negligible cost)
+- Cannot detect file-mode-only changes if josh normalizes modes (theoretical edge case)

docs/adr/010-onboard-checkpoint-resume.md

@@ -0,0 +1,76 @@
+# ADR-010: Onboard Workflow with Checkpoint/Resume
+
+**Status:** Accepted
+**Date:** 2026-02
+
+## Context
+
+Onboarding an existing subrepo into the monorepo is a multi-step process that involves human interaction (renaming repos, merging PRs). The full flow is:
+
+1. Prerequisites: rename existing repo, create new empty repo
+2. Import: copy subrepo content into monorepo, create import PR(s)
+3. Wait: human merges the import PR(s)
+4. Reset: force-push josh-filtered history to the new empty repo
+5. (Optional) Migrate open PRs from archived repo
+
+Each step can fail or be interrupted. The process may span hours or days (waiting for PR review). If interrupted, restarting from scratch wastes work and can create duplicate PRs.
+
+### Alternatives considered
+
+1. **Single-shot script**: Run all steps in sequence. If interrupted, must restart from scratch. Duplicate PRs if import step is re-run.
+
+2. **Manual step-by-step commands**: `import`, then manually run `reset`. Simple but error-prone — users may forget steps or run them out of order.
+
+3. **Checkpoint/resume with persistent state**: Track the current step and intermediate results (PR numbers, reset branches) in persistent state. On re-run, resume from the last completed step.
+
+## Decision
+
+Implement `josh-sync onboard` as a checkpoint/resume workflow with state stored on the `josh-sync-state` branch at `<target>/onboard.json`.
+
+### State machine
+
+```
+start → importing → waiting-for-merge → resetting → complete
+```
+
+Each transition is persisted before proceeding. Re-running `josh-sync onboard <target>` reads the current step and resumes.
+
+### State schema
+
+```json
+{
+  "step": "waiting-for-merge",
+  "archived_api": "https://host/api/v1/repos/org/repo-archived",
+  "archived_url": "git@host:org/repo-archived.git",
+  "archived_auth": "ssh",
+  "import_prs": { "main": 42 },
+  "reset_branches": ["main"],
+  "migrated_prs": [
+    { "old_number": 5, "new_number": 12, "title": "Fix login" }
+  ],
+  "timestamp": "2026-02-10T14:30:00Z"
+}
+```
+
+### Per-branch progress
+
+Import and reset both iterate over branches. Progress is saved after each branch, so interruption mid-iteration resumes at the next unprocessed branch.
+
+### PR migration
+
+`josh-sync migrate-pr` is a separate command that reads onboard state (for the archived repo URL) and tracks migrated PRs. It uses `git apply --3way` for resilient patch application — the subrepo's content is identical after reset, so patches apply cleanly.
+
+## Consequences
+
+**Positive:**
+- Safe to interrupt at any point — no duplicate work on resume
+- Per-branch tracking prevents duplicate import PRs or redundant resets
+- Archived repo URL stored in state — `migrate-pr` can operate independently
+- `--restart` flag allows starting over if state is corrupted
+- Human-friendly — prints instructions at each step
+
+**Negative:**
+- State management adds complexity (read/write onboard state, step validation)
+- Interactive steps (`read -r`) are not suitable for fully automated pipelines
+- Onboard state persists on the state branch even after completion (minor clutter)
+- The step machine is linear — cannot skip steps or run them out of order

docs/adr/011-linearize-fallback-reverse.md

@@ -0,0 +1,58 @@
+# ADR-011: Linearize Fallback for Reverse Sync
+
+**Status:** Accepted
+**Date:** 2026-03
+
+## Context
+
+Josh-proxy rejects reverse sync pushes when the subrepo history contains merge commits whose parents it cannot map through the filter. This happens when:
+
+1. A long-lived branch (e.g., `stage`) is merged into `main` via a merge commit
+2. That branch contains auto-sync merge commits or criss-cross merges with `main`
+3. Josh encounters the merge commit, tries to map both parents through the filter, and fails with a 500 error
+
+This is a legitimate subrepo workflow — teams merge staging branches into main regularly. The sync tool should handle it without requiring teams to change their Git workflow.
+
+### Alternatives considered
+
+1. **Squash all commits into one**: Simple but destroys all commit granularity.
+2. **Rewrite subrepo history**: Breaks josh's SHA mapping, forces all developers to re-clone.
+3. **Linearize: cherry-pick regular commits, squash only merges**: Preserves individual commit granularity; only merge commits lose their multi-parent structure.
+
+## Decision
+
+When the direct push through josh-proxy fails, fall back to option 4: linearize the history by cherry-picking onto the josh-filtered base.
+
+### How it works
+
+1. Direct `git push` through josh-proxy is attempted first (existing behavior)
+2. If it fails, create a temporary branch from `mono-filtered/<branch>`
+3. Walk human commits (oldest-first, bot commits excluded) from the ancestry path:
+   - **Regular commits** (≤1 parent): `git cherry-pick <sha>` — preserves author, date, and message
+   - **Merge commits** (>1 parent): `git cherry-pick -m 1 <sha>` — applies the merge's diff relative to its first parent as a single commit
+4. If cherry-pick conflicts (rare — usually due to ordering issues), fall back to `git diff | git apply` with the original author metadata
+5. Push the linearized branch through josh-proxy
+6. PR body includes a note explaining that merge commits were squashed
+
+### What is preserved
+
+- Individual non-merge commits (author, date, message, diff)
+- The net effect of each merge commit (as a squashed single commit)
+- The original commit list in the PR body for reference
+
+### What is lost
+
+- The multi-parent structure of merge commits (they become single-parent)
+- The distinction between "changes introduced by the merge" vs "changes from each parent" — the merge is represented as its diff from first parent
+
+## Consequences
+
+**Positive:**
+- Reverse sync no longer gets stuck on merge commits — handles the common case automatically
+- Non-merge commits retain full granularity (no unnecessary squashing)
+- Subrepo history is untouched — no rewriting, no broken sync relationship
+- The PR body documents when linearization was used, so reviewers know
+
+**Negative:**
+- Merge commit semantics are lost on the monorepo side (they appear as regular commits)
+- Adds complexity to the reverse sync path (two code paths: direct push and linearize fallback)

docs/adr/012-explicit-monorepo-url.md

@@ -0,0 +1,53 @@
+# ADR-012: Explicit `monorepo_url` (drop first-target-host inference)
+
+**Status:** Accepted
+**Date:** 2026-04
+
+## Context
+
+josh-sync v1.x had no first-class field for the monorepo's git location. To call the gitea PR API and to clone the monorepo for `initial_import` / force-push, the script derived the gitea host from the **first target's `subrepo_url`**:
+
+```bash
+# lib/config.sh (v1.x)
+gitea_host=$(echo "$JOSH_SYNC_TARGETS" | jq -r '.[0].gitea_host')
+export MONOREPO_API="${MONOREPO_API:-https://${gitea_host}/api/v1/repos/${MONOREPO_PATH}}"
+```
+
+This worked silently for every existing config — studio, kinanah/stores, itkan/sdlc — because in each, target 0's host happens to match the monorepo's host. The portal monorepo broke the assumption: monorepo on `code.atome.ac:atome-portal/portal`, single target `bff` on `code.itkan.io:sdlc/odoo_bff_core`. The derivation produced `https://code.itkan.io/atome-portal/portal.git` (host borrowed from the wrong target), giving a 404 on `josh-sync import`.
+
+Two issues stack:
+
+1. **Implicit coupling**: target ordering becomes load-bearing in a non-obvious way. The `MONOREPO_API` env var was the only escape hatch, hidden in shell init.
+2. **Asymmetry**: `subrepo_url` is declared explicitly per target with full SSH/HTTPS support; the monorepo had only a `monorepo_path` and was always cloned via HTTPS+token. Local users with SSH keys for the monorepo still had to provide a token.
+
+### Alternatives considered
+
+1. **Keep deriving, document the env override loudly.** Cheapest. Leaves the booby trap in place — still fails closed for any future cross-host config.
+2. **Add `josh.gitea_host` only.** Fixes the host issue without enabling SSH cloning of the monorepo. Half a fix, and asymmetric with how subrepos are declared.
+3. **Add `josh.monorepo_url` (full URL), mirror `subrepo_url` exactly.** Removes the inference; enables SSH clone; symmetric with subrepos. Breaking — every existing config needs to add the field.
+
+## Decision
+
+Add a required `josh.monorepo_url` field plus an optional `josh.monorepo_auth` (default `"https"`). Mirror the `subrepo_url` parsing and `subrepo_auth_url()` helper exactly:
+
+- `parse_config` extracts `MONOREPO_GITEA_HOST` and `MONOREPO_REPO_PATH` from `monorepo_url` using the same jq regex as `subrepo_url`.
+- `MONOREPO_API` derives from `MONOREPO_GITEA_HOST` instead of `.[0].gitea_host`. The env-var override stays as a real escape hatch (custom API endpoints).
+- `mono_auth_url()` in `lib/auth.sh` mirrors `subrepo_auth_url()`: SSH returns the bare URL, HTTPS injects `${BOT_USER}:${GITEA_TOKEN}@` (auto-converting `git@host:org/repo.git` to `https://host/org/repo.git` first).
+- `initial_import()` and the force-push path in `lib/sync.sh` call `mono_auth_url()` instead of constructing the URL inline from `MONOREPO_API`.
+
+The change is shipped as **v2.0.0** with `schema_version: 2` required. v1 configs are rejected with a migration pointer; configs missing `monorepo_url` are rejected with the field name and an example.
+
+## Consequences
+
+**Positive:**
+- No more first-target-ordering coupling. Add or reorder targets freely.
+- Multi-host setups (monorepo on host A, subrepo on host B) are first-class.
+- SSH clone of the monorepo works without a token (the user's ssh-agent / `~/.ssh/config` resolves the key). PR creation still needs `GITEA_TOKEN`.
+- Symmetric config: monorepo and subrepos both declare a URL + auth method.
+
+**Negative:**
+- Breaking change. Every existing config must add `schema_version: 2` and `josh.monorepo_url`. Mitigated by the validation `die`s pointing at the field name and changelog.
+- Two related-but-distinct fields (`monorepo_path` for the josh-proxy filter; `monorepo_url` for the gitea clone) — kept separate because josh-proxy's path may not always equal the gitea path in custom setups.
+
+**Risks:**
+- Users may set `monorepo_url` to a host that doesn't match their `proxy_url`'s upstream. Detection is out of scope for this ADR; a follow-up `josh-sync preflight` check could compare hosts and warn.

docs/adr/013-non-destructive-adoption.md

@@ -0,0 +1,56 @@
+# ADR-013: Non-destructive adoption merge for existing subrepos
+
+**Status:** Accepted
+**Date:** 2026-04
+**Update (2026-05):** The standalone `josh-sync adopt <target>` command described below has been folded into `josh-sync onboard <target>` as the `adopt` strategy (selectable via `--mode=adopt`, `targets[].history_lock: preserve`, or auto-detection when the subrepo has any branches). `josh-sync adopt` is retained as a thin CLI alias. The state file moved from `<target>/adopt.json` to `<target>/onboard.json` with a `.strategy` field; the legacy file is still read for backward compatibility. See the guide's Onboarding section.
+
+## Context
+
+Existing subrepos often already have real history, open PRs, and developer clones.
+The original `import` then `reset` onboarding path establishes Josh-compatible
+history by force-pushing the Josh-filtered monorepo history onto the subrepo.
+That is correct for empty replacement repos, but it rewrites the active subrepo
+branch and invalidates local clones.
+
+We need a path for active subrepos where history must remain available on the
+same branch and where open PR branches should stay based on the existing history.
+
+## Decision
+
+Add `josh-sync adopt <target>` as a separate workflow from `onboard` and `reset`.
+Adoption imports the subrepo content into the monorepo, waits for the import PR
+to merge, then creates one merge commit on each configured subrepo branch:
+
+1. First parent: Josh-filtered monorepo HEAD
+2. Second parent: existing subrepo HEAD
+3. Tree: Josh-filtered monorepo tree
+
+Josh follows first-parent history back to the monorepo, while Git still keeps
+the old subrepo history reachable through parent 2. The push is a normal
+fast-forward push from the existing subrepo HEAD to the adoption merge commit.
+No force-push is used.
+
+Before creating the adoption merge, josh-sync requires the existing subrepo tree
+to match the Josh-filtered monorepo tree. If the trees differ, adoption aborts
+and the user must merge the import PR or reconcile the branch contents first.
+
+Adoption state is stored separately at `<target>/adopt.json` on the
+`josh-sync-state` branch.
+
+## Consequences
+
+**Positive:**
+
+- Existing subrepo history remains on the active branch.
+- Existing clones can fast-forward instead of hard-resetting or re-cloning.
+- Open PR branches remain based on reachable history.
+- Josh-compatible ancestry is established without a destructive rewrite.
+
+**Negative:**
+
+- Adoption adds one synthetic merge commit to each adopted subrepo branch.
+- Strict "no subrepo commit at all" adoption is impossible if the existing
+  subrepo branch must become connected to the Josh-filtered history without a
+  rewrite. A commit is needed to join the two histories.
+- Tree equality is strict. If the monorepo import differs from the subrepo
+  content, adoption stops until the user resolves the mismatch.

docs/adr/README.md

@@ -0,0 +1,21 @@
+# Architecture Decision Records
+
+This directory contains Architecture Decision Records (ADRs) for josh-sync. Each ADR documents a significant design decision, its context, the alternatives considered, and the rationale for the chosen approach.
+
+## Index
+
+| ADR | Title | Status |
+|-----|-------|--------|
+| [001](001-josh-proxy-for-sync.md) | Josh-proxy for bidirectional sync | Accepted |
+| [002](002-state-on-orphan-branch.md) | State storage on orphan git branch | Accepted |
+| [003](003-force-with-lease-forward.md) | Force-with-lease for forward sync | Accepted |
+| [004](004-always-pr-reverse.md) | Always-PR policy for reverse sync | Accepted |
+| [005](005-git-trailer-loop-prevention.md) | Git trailer for loop prevention | Accepted |
+| [006](006-inline-exclude-filter.md) | Inline exclude in josh-proxy URL | Accepted |
+| [007](007-reconciliation-merge.md) | Reconciliation merge for filter changes | Accepted |
+| [008](008-first-parent-ordering.md) | First-parent ordering in reconciliation merges | Accepted |
+| [009](009-tree-comparison-guard.md) | Tree comparison as sync skip guard | Accepted |
+| [010](010-onboard-checkpoint-resume.md) | Onboard workflow with checkpoint/resume | Accepted |
+| [011](011-linearize-fallback-reverse.md) | Linearize fallback for reverse sync | Accepted |
+| [012](012-explicit-monorepo-url.md) | Explicit `monorepo_url` (drop first-target-host inference) | Accepted |
+| [013](013-non-destructive-adoption.md) | Non-destructive adoption merge for existing subrepos | Accepted |

docs/config-reference.md

@@ -5,17 +5,26 @@ Full reference for `.josh-sync.yml` fields and environment variables.
 ## `.josh-sync.yml` Structure
 
 ```yaml
-josh:       # josh-proxy settings (required)
+schema_version: 2   # required since v2.0.0
+josh:               # josh-proxy + monorepo settings (required)
 targets:            # sync targets (required, at least 1)
 bot:                # bot identity for sync commits (required)
 ```
 
+## `schema_version`
+
+| Type | Required | Description |
+|------|----------|-------------|
+| integer | Yes | Must be `2` for josh-sync v2.x configs. v1 configs are rejected; see [Changelog v2.0.0](../CHANGELOG.md#200) for migration. |
+
 ## `josh` Section
 
 | Field | Type | Required | Description |
 |-------|------|----------|-------------|
 | `proxy_url` | string | Yes | Josh-proxy URL, no trailing slash. Must start with `http://` or `https://`. |
 | `monorepo_path` | string | Yes | Repository path as josh-proxy sees it (e.g., `org/monorepo`). |
+| `monorepo_url` | string | Yes | Monorepo git clone URL — `git@host:org/repo.git` (SSH), `ssh://...`, or `https://host/org/repo.git`. The gitea host is derived from this URL and used for the PR API and direct clones, decoupled from any target's host. |
+| `monorepo_auth` | string | No (default `"https"`) | Clone auth method: `"https"` (injects `${SYNC_BOT_USER}:${SYNC_BOT_TOKEN}` into the URL) or `"ssh"` (uses the user's ssh-agent / `~/.ssh/config`). PR creation always uses `GITEA_TOKEN` regardless. |
 
 ## `targets[]` Section
 
@@ -32,6 +41,8 @@ Each target maps a monorepo subfolder to an external subrepo.
 | `subrepo_ssh_key_var` | string | No | `"SUBREPO_SSH_KEY"` | Name of the env var holding the SSH private key for this target. |
 | `branches` | object | Yes | — | Branch mapping: `mono_branch: subrepo_branch`. Each key-value pair syncs those branches bidirectionally. |
 | `forward_only` | string[] | No | `[]` | Branches that only sync mono → subrepo, never reverse. |
+| `exclude` | string[] | No | `[]` | File/directory patterns to exclude from sync via josh `:exclude` filter. Excluded files exist only in the monorepo, never in the subrepo. See [Excluding Files](guide.md#excluding-files-from-sync). |
+| `history_lock` | string | No | (auto-detect) | Onboarding strategy hint. `"preserve"` selects the non-destructive [adopt](guide.md#onboarding) strategy (keeps subrepo history via an adoption merge — ADR-013); `"rewrite"` selects the destructive reset strategy (force-pushes josh-filtered history). When omitted, `josh-sync onboard` auto-detects: subrepos with branches → adopt, empty subrepos → reset. The CLI flag `--mode={reset,adopt}` overrides this. |
 
 ## `bot` Section
 
@@ -72,7 +83,7 @@ targets:
 | `JOSH_SYNC_TARGET` | Restrict sync to a single target | All targets |
 | `JOSH_SYNC_STATE_BRANCH` | Name of the orphan branch for state storage | `josh-sync-state` |
 | `JOSH_SYNC_DEBUG` | Enable verbose logging (`1` to enable) | `0` |
-| `MONOREPO_API` | Override monorepo API URL | Auto-derived from first target's host |
+| `MONOREPO_API` | Override the monorepo gitea PR API URL. Escape hatch for custom API endpoints; rarely needed. | `https://{monorepo_url's host}/api/v1/repos/{monorepo_path}` |
 
 ## JSON Schema
 

docs/guide.md

@@ -78,9 +78,13 @@ git ls-remote https://josh.example.com/org/monorepo.git HEAD
 Create `.josh-sync.yml` at the monorepo root. Each target maps a monorepo subfolder to an external subrepo:
 
 ```yaml
+schema_version: 2
+
 josh:
   proxy_url: "https://josh.example.com"     # josh-proxy URL (no trailing slash)
-  monorepo_path: "org/monorepo"              # repo path as josh sees it
+  monorepo_path: "org/monorepo"              # repo path as josh-proxy sees it
+  monorepo_url: "git@gitea.example.com:org/monorepo.git"  # monorepo git clone URL
+  monorepo_auth: "ssh"                       # optional, default "https"
 
 targets:
   - name: "billing"                          # unique identifier
@@ -91,6 +95,9 @@ targets:
     branches:
       main: main                             # mono_branch: subrepo_branch
     forward_only: []
+    exclude:                                 # files excluded from subrepo (optional)
+      - ".monorepo/"                         # monorepo-only config dir
+      - "**/internal/"                       # internal dirs at any depth
 
   - name: "auth"
     subfolder: "services/auth"
@@ -183,7 +190,7 @@ To pin to a specific version, use a tag ref in `devenv.yaml`:
 
 ```yaml
 josh-sync:
-  url: git+https://your-gitea.example.com/org/josh-sync?ref=v1.1
+  url: git+https://your-gitea.example.com/org/josh-sync?ref=refs/tags/v1.2
   flake: true
 ```
 
@@ -215,16 +222,53 @@ This validates:
 
 For a new monorepo before import, preflight may warn that subfolders don't exist yet — that's expected.
 
-## Step 5: Import Existing Subrepos
+## Step 5: Onboard Existing Subrepos
 
-This is the critical onboarding step. There are two approaches:
+`josh-sync onboard <target>` is the single entry point for connecting an existing subrepo to the monorepo. It runs interactively with checkpoint/resume and picks one of two strategies:
 
-- **`josh-sync onboard`** (recommended) — interactive, resumable, preserves open PRs
-- **Manual `import` → merge → `reset`** — lower-level, for automation or when there are no open PRs to preserve
+- **adopt** (non-destructive) — keeps the subrepo's existing history and joins it to josh-filtered history via a single adoption merge commit. No force-push. Developers fast-forward; open PR branches stay valid.
+- **reset** (destructive) — force-pushes josh-filtered history onto the subrepo, replacing its prior history. Use this for empty replacement repos (typically paired with renaming the old repo to `*-archived`).
 
-### Option A: Onboard (recommended)
+### Strategy selection
 
-The `onboard` command walks you through the entire process interactively, with checkpoint/resume at every step.
+`josh-sync onboard` resolves the strategy in this order (highest precedence first):
+
+1. **CLI flag** — `--mode=adopt` or `--mode=reset` overrides everything.
+2. **Config** — `targets[].history_lock: preserve` selects adopt; `rewrite` selects reset.
+3. **Auto-detect** — `git ls-remote --heads` on the subrepo. Branches present → adopt. Empty repo → reset.
+
+The chosen strategy is logged at preflight so you can see what will happen before any side effects.
+
+`josh-sync adopt <target>` is kept as a back-compat alias for `josh-sync onboard --mode=adopt`.
+
+### Adopt strategy (auto-selected for active subrepos)
+
+```bash
+josh-sync onboard billing                # auto-detect — picks adopt for non-empty subrepo
+josh-sync onboard billing --mode=adopt   # force adopt explicitly
+josh-sync adopt billing                  # equivalent back-compat alias
+```
+
+The command will:
+1. **Import** — copies current subrepo content into the monorepo and creates import PRs (one per branch)
+2. **Wait for merge** — shows PR numbers and waits for you to merge them
+3. **Verify trees** — requires the existing subrepo tree to match the Josh-filtered monorepo tree
+4. **Adopt** — creates a merge commit on the subrepo with Josh-filtered HEAD as parent 1 and existing subrepo HEAD as parent 2
+5. **Push** — pushes the adoption merge with a normal fast-forward push, never force-push
+
+The adoption merge preserves the old subrepo history while giving Josh a first-parent path back to the monorepo. If interrupted, re-run `josh-sync onboard billing` to resume. Use `--restart` to start over. See [ADR-013](adr/013-non-destructive-adoption.md) for the design rationale.
+
+After adoption, developers can update existing clones with a normal fast-forward:
+
+```bash
+git fetch origin
+git checkout main
+git merge --ff-only origin/main
+```
+
+### Reset strategy (auto-selected for empty replacement repos)
+
+Use the reset strategy when you intentionally want to archive the old subrepo and start fresh from a new empty repo.
 
 **Before you start:**
 
@@ -236,7 +280,8 @@ The rename preserves the archived repo with all its history and open PRs. The ne
 **Run onboard:**
 
 ```bash
-josh-sync onboard billing
+josh-sync onboard billing                # auto-detect — picks reset for empty subrepo
+josh-sync onboard billing --mode=reset   # force reset explicitly
 ```
 
 The command will:
@@ -265,13 +310,13 @@ josh-sync migrate-pr billing 5 8 12
 
 PR migration works by fetching the diff from the archived repo's PR, applying it to the new repo, and creating a new PR. File content is identical after reset, so patches apply cleanly.
 
-### Option B: Manual import → merge → reset
+### Manual: import → merge → reset
 
-Use this when the subrepo has no open PRs to preserve, or for scripted automation.
+Use this for scripted automation or when you intentionally want to replace subrepo history without the interactive wrapper.
 
 > Do this **one target at a time** to keep PRs reviewable.
 
-#### 5b-1. Import
+#### Manual: Import
 
 ```bash
 josh-sync import billing
@@ -286,13 +331,13 @@ This:
 
 Review the import PR — check for leaked credentials, environment-specific config, or files that shouldn't be in the monorepo.
 
-#### 5b-2. Merge the import PR
+#### Manual: Merge the import PR
 
 Merge the PR using your Git platform's UI. This lands the subrepo content into the monorepo's main branch.
 
 > At this point, the monorepo has the content but the histories are disconnected. Sync will **not** work until you complete the reset step.
 
-#### 5b-3. Reset
+#### Manual: Reset
 
 ```bash
 josh-sync reset billing
@@ -319,7 +364,7 @@ git checkout stage && git reset --hard origin/stage   # repeat for each branch
 
 Or simply delete and re-clone the subrepo. Local-only branches (not pushed to the remote) will be lost either way.
 
-#### 5b-4. Repeat for each target
+#### Manual: Repeat for each target
 
 ```
 For each target:
@@ -330,13 +375,13 @@ For each target:
 
 ### Verify
 
-After all targets are imported and reset (whichever option you used):
+After all targets are adopted or reset:
 
 ```bash
 # Check all targets show state
 josh-sync status
 
-# Test forward sync — should return "skip" (trees are identical after reset)
+# Test forward sync — should return "skip" (trees are identical after adoption/reset)
 josh-sync sync --forward --target billing
 
 # Test reverse sync — should return "skip" (no new human commits)
@@ -509,12 +554,105 @@ Runs on a cron schedule (never triggered by subrepo pushes):
 
 ### Loop prevention
 
-Bot commits include a git trailer like `Josh-Sync-Origin: forward/main/2024-02-12T10:30:00Z`. Each sync direction filters out commits with this trailer, preventing changes from bouncing back and forth. The CI action also has a loop guard that skips entirely if the HEAD commit has the trailer.
+Bot commits include a git trailer like `Josh-Sync-Origin: forward/main/2024-02-12T10:30:00Z`. Reverse sync filters out commits with this trailer, preventing changes from bouncing back from the target repo into the source repo.
+
+The CI action does not skip forward sync solely because the checked-out HEAD commit has a sync trailer. A repo can be a valid middle hop: it may receive a sync commit from one repository and still need to forward its filtered subtree to another repository. Forward sync relies on tree comparison, sync state, and merge checks to decide whether anything should be pushed.
 
 ### State tracking
 
 Sync state is stored as JSON files on an orphan branch (`josh-sync-state`), one file per target/branch. This tracks the last-synced commit SHAs and timestamps to avoid re-syncing the same changes.
 
+## Recommended Git Workflow
+
+Josh-proxy maps commits through a filter per-branch. It handles linear history and simple merges (short-lived feature branches) without issues. However, it **cannot map merge commits whose parents were created on the subrepo side** — because those commits were never pushed through josh and have no monorepo-side mapping.
+
+This means cross-branch merges (e.g., `stage` → `main`) must happen on the monorepo side, where josh can filter the result cleanly.
+
+### The rule
+
+**The monorepo owns branch topology. The subrepo owns feature development.**
+
+### What to do where
+
+| Action | Where to do it | Why |
+|--------|---------------|-----|
+| Feature branch → `main` | **Subrepo** (PR, any merge strategy) | Short-lived branch with clean lineage — josh handles it |
+| `stage` → `main` (promotion) | **Monorepo** | Cross-branch merge — forward sync propagates the result to both subrepo branches |
+| `main` → `stage` (catch-up) | **Monorepo** | Same reason — avoids criss-cross merge history on subrepo |
+| Hotfix to `main` | **Either side** | Single commit or small PR — works everywhere |
+| Config/CI changes (monorepo-only) | **Monorepo** | Not synced to subrepo (use `exclude` for monorepo-only files) |
+
+### What to avoid
+
+- **Don't merge `stage` into `main` on the subrepo with a merge commit.** The merge parents include commits created on the subrepo side (forward sync merges, criss-cross merges) that josh has no mapping for. Josh rejects the push with a 500 error.
+- **Don't merge `main` into `stage` on the subrepo.** Creates criss-cross merge history that causes the same josh mapping failure when `stage` is later merged back.
+- **Don't rebase synced branches on the subrepo.** This rewrites commit SHAs that josh has already mapped, breaking the sync relationship.
+
+### If you must merge cross-branch on the subrepo
+
+Use a **squash merge**. A squash merge produces a single commit with one parent — josh can always map it. You lose the individual commit history on the target branch, but the sync goes through cleanly.
+
+As a safety net, josh-sync automatically falls back to linearizing the history when josh rejects a push — cherry-picking regular commits individually and squashing only the problematic merge commits. See the [troubleshooting section](#josh-rejected-push-reverse-sync) and [ADR-011](adr/011-linearize-fallback-reverse.md).
+
+## Excluding Files from Sync
+
+Some files in the monorepo subfolder may not belong in the subrepo (e.g., monorepo-specific CI configs, internal tooling). The `exclude` config field removes these at the josh-proxy layer — excluded files never appear in the subrepo.
+
+### Configuration
+
+Add an `exclude` list to any target:
+
+```yaml
+targets:
+  - name: "billing"
+    subfolder: "services/billing"
+    subrepo_url: "git@host:org/billing.git"
+    exclude:
+      - ".monorepo/"          # directory at subfolder root
+      - "**/internal/"        # directory at any depth
+      - "*.secret"            # files by extension
+    branches:
+      main: main
+```
+
+### How it works
+
+When `exclude` is present, josh-sync appends an inline `:exclude` filter to the josh-proxy URL. For the example above, the josh filter becomes:
+
+```
+:/services/billing:exclude[::.monorepo/,::**/internal/,::*.secret]
+```
+
+Josh-proxy applies this filter at the transport layer — no extra files to generate or commit. This means:
+- **Forward sync**: the filtered clone already excludes the files
+- **Reverse sync**: pushes through josh also respect the exclusion
+- **Reset**: the subrepo history never contains excluded files
+- **Tree comparison**: `skip` detection works correctly (excluded files are not in the diff)
+
+### Pattern syntax
+
+Josh uses `::` patterns inside `:exclude[...]`:
+
+| Pattern | Matches |
+|---------|---------|
+| `dir/` | Directory at subfolder root |
+| `file` | File at subfolder root |
+| `**/dir/` | Directory at any depth |
+| `**/file` | File at any depth |
+| `*.ext` | Glob pattern (single `*` only) |
+
+### Setup
+
+1. Add `exclude` to the target in `.josh-sync.yml`
+2. Run `josh-sync preflight` to verify the filter works
+3. Forward sync will now exclude the specified files
+
+No extra files to generate or commit — the exclusion is embedded directly in the josh-proxy URL.
+
+### Changing the exclude list
+
+You can safely add or remove patterns from `exclude` at any time. When josh-sync detects that the filter has changed since the last sync, it automatically creates a reconciliation merge commit on the subrepo that connects the old and new histories — no manual reset or force-push required. Developers do not need to re-clone the subrepo.
+
 ## Adding a New Target
 
 To add a new subrepo after initial setup:
@@ -522,12 +660,13 @@ To add a new subrepo after initial setup:
 1. Add the target to `.josh-sync.yml`
 2. Update the forward workflow's `paths:` list to include the new subfolder
 3. Commit and push
-4. Import the target:
+4. Onboard the target — `josh-sync onboard` auto-picks `adopt` for non-empty subrepos and `reset` for empty ones; override with `--mode={reset,adopt}` or pin via the target's `history_lock` config field.
    ```bash
-   # Recommended: interactive onboard (preserves open PRs)
-   josh-sync onboard new-target
+   josh-sync onboard new-target                # auto-detect strategy
+   josh-sync onboard new-target --mode=adopt   # force adopt
+   josh-sync onboard new-target --mode=reset   # force reset
 
-   # Or manual: import → merge PR → reset
+   # Manual lower-level path (when scripting):
    josh-sync import new-target
    # merge the PR
    josh-sync reset new-target
@@ -554,7 +693,35 @@ Normal: the subrepo changed while sync was running. The next sync run will pick
 
 ### "Josh rejected push" (reverse sync)
 
-Josh-proxy couldn't map the push back to the monorepo. Check josh-proxy logs, verify the josh filter is correct. May indicate a history divergence — consider running `josh-sync reset <target>`.
+Josh-proxy couldn't map the push back to the monorepo. This has two common causes:
+
+#### Merge commits with unmappable parents
+
+**Symptom:** Josh returns `500 Internal Server Error` with a message like:
+
+```
+rejecting merge with 2 parents:
+"Merge pull request 'stage' (#30) from stage into main" (c4fa3c9...)
+1) "Merge branch 'auto-sync/import-...'" (4bf8704...)
+2) "Merge branch 'main' into stage" (d021654...)
+```
+
+**Cause:** The subrepo has a merge commit whose parents josh-proxy cannot trace through its filter. This typically happens when:
+- A long-lived branch (e.g., `stage`) is merged into `main` via a merge commit (not squash)
+- That branch contains auto-sync merge commits or other history that doesn't exist in josh's filtered view
+- Someone merges `main` into a feature/staging branch and then merges it back — the criss-cross parents confuse josh's mapping
+
+**Automatic handling:** josh-sync automatically falls back to linearizing the history when the direct push fails. Regular commits are cherry-picked individually (preserving authorship and messages), while merge commits are squashed into single commits via `cherry-pick -m 1`. The PR notes when this fallback was used. See [ADR-011](adr/011-linearize-fallback-reverse.md).
+
+**Prevention:** In josh-synced subrepos, prefer **squash merges** when merging long-lived branches (stage, develop) into the synced branch. Squash merges produce a single commit with no merge parents, which josh can always map. Regular feature branch merges (short-lived, no auto-sync history) are usually fine.
+
+**Manual resolution (if automatic fallback also fails):** This indicates a more fundamental history issue. Options:
+1. Cherry-pick the desired changes manually onto a clean branch and push through josh
+2. Run `josh-sync reset <target>` to re-establish history (destructive — all subrepo clones must re-fetch)
+
+#### Filter or path mismatch
+
+Josh-proxy couldn't map the push due to an incorrect filter. Check josh-proxy logs, verify the `josh_filter` or `subfolder` in `.josh-sync.yml` is correct, and ensure the subfolder exists in the monorepo.
 
 ### Import PR shows "No changes"
 

examples/devenv.nix

@@ -5,12 +5,12 @@
 # In devenv.yaml:
 #   inputs:
 #     josh-sync:
-#       url: github:org/josh-sync/v1.0.0
+#       url: git+https://your-gitea.example.com/org/josh-sync?ref=refs/tags/v1.2
 #       flake: true
 #
 # Or in flake.nix:
 #   inputs.josh-sync = {
-#     url = "github:org/josh-sync/v1.0.0";
+#     url = "git+https://your-gitea.example.com/org/josh-sync?ref=refs/tags/v1.2";
 #     inputs.nixpkgs.follows = "nixpkgs";
 #   };
 
@@ -26,6 +26,8 @@
   #   josh-sync preflight              Validate config and connectivity
   #   josh-sync import <target>        Initial import from subrepo
   #   josh-sync reset <target>         Reset subrepo to josh-filtered view
+  #   josh-sync onboard <target>       Interactive import + reset workflow
+  #   josh-sync migrate-pr <target>    Migrate PRs from archived repo
   #   josh-sync status                 Show target config and sync state
   #   josh-sync state show <t> [b]     Show state JSON
   #   josh-sync state reset <t> [b]    Reset state

examples/forward.yml

@@ -62,7 +62,7 @@ jobs:
               done | sort -u | paste -sd ',' -)
           echo "targets=${TARGETS}" >> "$GITHUB_OUTPUT"
 
-      - uses: https://your-gitea.example.com/org/josh-sync@v1
+      - uses: https://your-gitea.example.com/org/josh-sync@v1.2
         with:
           direction: forward
           target: ${{ github.event.inputs.target || steps.detect.outputs.targets }}

examples/josh-sync.yml

@@ -1,26 +1,39 @@
 # .josh-sync.yml — Multi-target configuration example
 # Place this at the root of your monorepo.
 
+# Required since v2.0.0. Bump alongside the josh-sync major version when
+# breaking config changes ship.
+schema_version: 2
+
 josh:
   # Your josh-proxy instance URL (no trailing slash)
   proxy_url: "https://josh.example.com"
-  # Repo path as josh sees it (org/repo on your Gitea/GitHub)
+  # Repo path as josh-proxy sees it (org/repo)
   monorepo_path: "org/monorepo"
+  # Monorepo git clone URL — git@host:org/repo.git (SSH) or https://host/org/repo.git.
+  # The gitea host is derived from this URL (used for the PR API and direct clones).
+  # The monorepo and any subrepo may live on different gitea hosts.
+  monorepo_url: "git@gitea.example.com:org/monorepo.git"
+  # Optional. Default "https". Use "ssh" to clone the monorepo via SSH (no token
+  # needed for the clone — PR creation still requires GITEA_TOKEN).
+  monorepo_auth: "ssh"
 
 targets:
   - name: "billing"
     subfolder: "services/billing"
-    josh_filter: ":/services/billing"
+    # josh_filter auto-derived as ":/services/billing" if omitted
     subrepo_url: "https://gitea.example.com/ext/billing.git"
     subrepo_auth: "https"
     branches:
       main: main
       develop: develop
     forward_only: []
+    exclude:                          # files excluded from subrepo (optional)
+      - ".monorepo/"                  # directory at subfolder root
+      - "**/internal/"                # directory at any depth
 
   - name: "auth"
     subfolder: "services/auth"
-    josh_filter: ":/services/auth"
     subrepo_url: "git@gitea.example.com:ext/auth.git"
     subrepo_auth: "ssh"
     # Per-target credential override (reads from $AUTH_SSH_KEY instead of $SUBREPO_SSH_KEY)
@@ -31,7 +44,6 @@ targets:
 
   - name: "shared-lib"
     subfolder: "libs/shared"
-    josh_filter: ":/libs/shared"
     subrepo_url: "https://gitea.example.com/ext/shared-lib.git"
     branches:
       main: main

examples/reverse.yml

@@ -40,7 +40,7 @@ jobs:
           curl -sL "https://github.com/mikefarah/yq/releases/download/v4.44.6/yq_linux_amd64" \
             -o /usr/local/bin/yq && chmod +x /usr/local/bin/yq
 
-      - uses: https://your-gitea.example.com/org/josh-sync@v1
+      - uses: https://your-gitea.example.com/org/josh-sync@v1.2
         with:
           direction: reverse
           target: ${{ github.event.inputs.target || '' }}

lib/adopt.sh

@@ -0,0 +1,109 @@
+#!/usr/bin/env bash
+# lib/adopt.sh — Non-destructive adoption merge primitive
+#
+# Provides:
+#   adopt_branch() — Create one adoption merge commit and push it fast-forward
+#
+# The orchestration (state machine, import → wait → finalize) lives in
+# lib/onboard.sh under strategy="adopt". `josh-sync adopt` is now a CLI alias
+# for `josh-sync onboard --mode=adopt`; see ADR-013 for design rationale.
+#
+# Requires: lib/core.sh, lib/config.sh, lib/auth.sh sourced
+
+# ─── Adopt Branch ────────────────────────────────────────────────
+# Establishes shared ancestry without rewriting the existing subrepo branch.
+#
+# Preconditions:
+# - The subrepo branch and josh-filtered monorepo branch must have identical trees.
+#
+# Resulting commit:
+# - parent 1: josh-filtered HEAD, so josh can follow first-parent history
+# - parent 2: existing subrepo HEAD, so old subrepo history stays reachable
+# - tree:     josh-filtered tree
+#
+# Returns: adopted | already-adopted | tree-mismatch | push-rejected | missing-branch
+
+adopt_branch() (
+  # Subshell function: contains the function-level EXIT trap, the internal cd,
+  # and any set -e propagation so it cannot pollute the caller's shell. Without
+  # this, the trap below would clobber callers' EXIT handlers (bats's own test
+  # reporting in particular silently disappears).
+  local mono_branch="$SYNC_BRANCH_MONO"
+  local subrepo_branch="$SYNC_BRANCH_SUBREPO"
+  local work_dir
+  work_dir=$(mktemp -d)
+  # shellcheck disable=SC2064  # Intentional early expansion — work_dir is local
+  trap "rm -rf '$work_dir'" EXIT
+
+  log "INFO" "=== Adopt: subrepo/${subrepo_branch} ↔ mono/${mono_branch} ==="
+
+  local remote_subrepo_sha
+  remote_subrepo_sha=$(git ls-remote "$(subrepo_auth_url)" "refs/heads/${subrepo_branch}" | awk '{print $1}') \
+    || die "Failed to reach subrepo (check SSH key / auth)"
+  if [ -z "$remote_subrepo_sha" ]; then
+    log "ERROR" "Subrepo branch ${subrepo_branch} does not exist"
+    echo "missing-branch"
+    return
+  fi
+
+  git clone "$(subrepo_auth_url)" \
+    --branch "$subrepo_branch" --single-branch \
+    "${work_dir}/subrepo" || die "Failed to clone subrepo"
+
+  cd "${work_dir}/subrepo" || exit
+  git config user.name "$BOT_NAME"
+  git config user.email "$BOT_EMAIL"
+
+  local subrepo_head subrepo_tree
+  subrepo_head=$(git rev-parse HEAD)
+  # shellcheck disable=SC1083  # {tree} is git syntax, not shell brace expansion
+  subrepo_tree=$(git rev-parse "HEAD^{tree}")
+  log "INFO" "Subrepo HEAD: ${subrepo_head:0:12}"
+
+  git remote add josh-filtered "$(josh_auth_url)"
+  git fetch josh-filtered "$mono_branch" || die "Failed to fetch from josh-proxy"
+
+  local josh_head josh_tree
+  josh_head=$(git rev-parse "josh-filtered/${mono_branch}")
+  # shellcheck disable=SC1083
+  josh_tree=$(git rev-parse "josh-filtered/${mono_branch}^{tree}")
+  log "INFO" "Josh-filtered HEAD: ${josh_head:0:12}"
+
+  if [ "$subrepo_tree" != "$josh_tree" ]; then
+    log "ERROR" "Tree mismatch: merge the import PR and ensure subrepo/${subrepo_branch} matches mono/${mono_branch} before adopting"
+    echo "tree-mismatch"
+    return
+  fi
+
+  if git merge-base --is-ancestor "$josh_head" "$subrepo_head" \
+    && git merge-base --is-ancestor "$subrepo_head" "$josh_head"; then
+    log "INFO" "Subrepo and josh-filtered histories already point to the same commit"
+    echo "already-adopted"
+    return
+  fi
+
+  if git merge-base --is-ancestor "$josh_head" "$subrepo_head"; then
+    log "INFO" "Josh-filtered HEAD is already an ancestor of subrepo HEAD"
+    echo "already-adopted"
+    return
+  fi
+
+  local merge_commit
+  merge_commit=$(git commit-tree "$josh_tree" \
+    -p "$josh_head" \
+    -p "$subrepo_head" \
+    -m "Adopt ${JOSH_SYNC_TARGET_NAME} for josh-sync
+
+${BOT_TRAILER}: adopt/${mono_branch}/$(date -u +%Y-%m-%dT%H:%M:%SZ)")
+
+  git reset --hard "$merge_commit" >&2
+  log "INFO" "Created adoption merge: ${merge_commit:0:12}"
+
+  if git push "$(subrepo_auth_url)" "HEAD:refs/heads/${subrepo_branch}"; then
+    log "INFO" "Adoption complete: pushed fast-forward merge to subrepo/${subrepo_branch}"
+    echo "adopted"
+  else
+    log "WARN" "Fast-forward push rejected — subrepo changed during adoption"
+    echo "push-rejected"
+  fi
+)

lib/auth.sh

@@ -2,7 +2,8 @@
 # lib/auth.sh — Authenticated URLs, remote queries, and PR creation
 #
 # Requires: lib/core.sh and lib/config.sh sourced first
-# Expects: JOSH_PROXY_URL, MONOREPO_PATH, BOT_USER, GITEA_TOKEN, JOSH_FILTER,
+# Expects: JOSH_PROXY_URL, MONOREPO_PATH, MONOREPO_URL, MONOREPO_AUTH,
+#           BOT_USER, GITEA_TOKEN, JOSH_FILTER,
 #           SUBREPO_URL, SUBREPO_AUTH, SUBREPO_TOKEN (set by parse_config + load_target)
 
 # ─── Josh-Proxy Auth URL ───────────────────────────────────────────
@@ -28,6 +29,27 @@ subrepo_auth_url() {
   fi
 }
 
+# ─── Monorepo Auth URL ─────────────────────────────────────────────
+# HTTPS: injects user:token into MONOREPO_URL (auto-converts git@ form to https)
+# SSH:   returns bare MONOREPO_URL (auth via user's ssh-agent / ~/.ssh/config,
+#        or via GIT_SSH_COMMAND if the caller wired one up for the monorepo host)
+
+mono_auth_url() {
+  if [ "${MONOREPO_AUTH:-https}" = "ssh" ]; then
+    echo "$MONOREPO_URL"
+  else
+    local https_url="$MONOREPO_URL"
+    # Convert git@host:org/repo.git → https://host/org/repo.git so token injection works
+    if [[ "$https_url" == git@* ]]; then
+      https_url=$(echo "$https_url" | sed -E 's|^git@([^:]+):(.+)$|https://\1/\2|')
+    elif [[ "$https_url" == ssh://* ]]; then
+      https_url=$(echo "$https_url" | sed -E 's|^ssh://[^@]*@([^/]+)/(.+)$|https://\1/\2|')
+    fi
+    # shellcheck disable=SC2001
+    echo "$https_url" | sed "s|https://|https://${BOT_USER}:${GITEA_TOKEN}@|"
+  fi
+}
+
 # ─── Remote Queries ─────────────────────────────────────────────────
 
 subrepo_ls_remote() {

lib/config.sh

@@ -16,11 +16,21 @@ parse_config() {
   local config_json
   config_json=$(yq -o json "$config_file") || die "Failed to parse ${config_file}"
 
+  # Schema version check — required, must be 2 (v1 configs are no longer supported)
+  local schema_version
+  schema_version=$(echo "$config_json" | jq -r '.schema_version // empty')
+  [ -n "$schema_version" ] || die "schema_version missing in ${config_file} (required since v2.0.0 — set 'schema_version: 2' at the top of the file; see CHANGELOG.md for migration instructions)"
+  [ "$schema_version" = "2" ] || die "Unsupported schema_version ${schema_version} in ${config_file} (this version of josh-sync requires schema_version 2 — see CHANGELOG.md for migration instructions)"
+
   # Export global values
   export JOSH_PROXY_URL
   JOSH_PROXY_URL=$(echo "$config_json" | jq -r '.josh.proxy_url')
   export MONOREPO_PATH
   MONOREPO_PATH=$(echo "$config_json" | jq -r '.josh.monorepo_path')
+  export MONOREPO_URL
+  MONOREPO_URL=$(echo "$config_json" | jq -r '.josh.monorepo_url')
+  export MONOREPO_AUTH
+  MONOREPO_AUTH=$(echo "$config_json" | jq -r '.josh.monorepo_auth // "https"')
   export BOT_NAME
   BOT_NAME=$(echo "$config_json" | jq -r '.bot.name')
   export BOT_EMAIL
@@ -30,13 +40,35 @@ parse_config() {
 
   [ -n "$JOSH_PROXY_URL" ] && [ "$JOSH_PROXY_URL" != "null" ] || die "josh.proxy_url missing in config"
   [ -n "$MONOREPO_PATH" ] && [ "$MONOREPO_PATH" != "null" ] || die "josh.monorepo_path missing in config"
+  [ -n "$MONOREPO_URL" ] && [ "$MONOREPO_URL" != "null" ] || die "josh.monorepo_url is required (added in schema_version 2). Set it to your monorepo's git clone URL, e.g. 'git@code.example.io:org/repo.git'."
+  [ "$MONOREPO_AUTH" = "ssh" ] || [ "$MONOREPO_AUTH" = "https" ] || die "josh.monorepo_auth must be 'ssh' or 'https' (got '${MONOREPO_AUTH}')"
   [ -n "$BOT_TRAILER" ] && [ "$BOT_TRAILER" != "null" ] || die "bot.trailer missing in config"
 
+  # Derive monorepo gitea_host and repo_path from monorepo_url (mirrors target derivation below)
+  local monorepo_meta
+  monorepo_meta=$(jq -nr --arg url "$MONOREPO_URL" '
+    $url as $u |
+    if ($u | test("^ssh://")) then
+      ($u | capture("ssh://[^@]*@(?<h>[^/]+)/(?<p>.+?)(\\.git)?$") // {h: "", p: ""})
+    elif ($u | test("^git@")) then
+      ($u | capture("git@(?<h>[^:/]+)[:/](?<p>.+?)(\\.git)?$") // {h: "", p: ""})
+    elif ($u | test("^https?://")) then
+      ($u | capture("https?://(?<h>[^/]+)/(?<p>.+?)(\\.git)?$") // {h: "", p: ""})
+    else
+      {h: "", p: ""}
+    end | "\(.h) \(.p)"')
+  export MONOREPO_GITEA_HOST="${monorepo_meta% *}"
+  export MONOREPO_REPO_PATH="${monorepo_meta#* }"
+  [ -n "$MONOREPO_GITEA_HOST" ] || die "Could not derive gitea host from josh.monorepo_url='${MONOREPO_URL}' (expected git@host:org/repo.git or https://host/org/repo.git)"
+
   # Enrich targets with derived fields (gitea_host, subrepo_repo_path, auto josh_filter)
   export JOSH_SYNC_TARGETS
   JOSH_SYNC_TARGETS=$(echo "$config_json" | jq '[.targets[] | . +
     # Auto-derive josh_filter from subfolder if not set
-    (if (.josh_filter // "") == "" then
+    # When exclude patterns are present, append inline :exclude[::p1,::p2,...] to the filter
+    (if (.exclude // [] | length) > 0 then
+      {josh_filter: (":/" + .subfolder + ":exclude[" + (.exclude | map("::" + .) | join(",")) + "]")}
+    elif (.josh_filter // "") == "" then
       {josh_filter: (":/" + .subfolder)}
     else {} end) +
     # Derive gitea_host and subrepo_repo_path from subrepo_url
@@ -56,6 +88,15 @@ parse_config() {
     )
   ]')
 
+  # Validate targets[].history_lock against the schema enum (preserve|rewrite).
+  # Caught at config parse time so typos don't sit silently until `onboard` runs.
+  local bad_lock
+  bad_lock=$(echo "$JOSH_SYNC_TARGETS" | jq -r '
+    .[] | select(.history_lock != null)
+        | select(.history_lock != "preserve" and .history_lock != "rewrite")
+        | "\(.name): \(.history_lock)"' | head -1)
+  [ -z "$bad_lock" ] || die "Invalid targets[].history_lock value (must be 'preserve' or 'rewrite'): ${bad_lock}"
+
   # Load .env credentials (if present, not required — CI sets these via secrets)
   if [ -f .env ]; then
     # shellcheck source=/dev/null
@@ -65,10 +106,8 @@ parse_config() {
   export GITEA_TOKEN="${GITEA_TOKEN:-${SYNC_BOT_TOKEN:-}}"
   export BOT_USER="${BOT_USER:-${SYNC_BOT_USER:-}}"
 
-  # Monorepo API URL (derived from first target's host, overridable via env)
-  local gitea_host
-  gitea_host=$(echo "$JOSH_SYNC_TARGETS" | jq -r '.[0].gitea_host')
-  export MONOREPO_API="${MONOREPO_API:-https://${gitea_host}/api/v1/repos/${MONOREPO_PATH}}"
+  # Monorepo API URL (derived from monorepo_url's host, overridable via env for custom API endpoints)
+  export MONOREPO_API="${MONOREPO_API:-https://${MONOREPO_GITEA_HOST}/api/v1/repos/${MONOREPO_PATH}}"
 
   log "INFO" "Config loaded: $(echo "$JOSH_SYNC_TARGETS" | jq 'length') target(s)"
 }

lib/onboard.sh

@@ -1,23 +1,56 @@
 #!/usr/bin/env bash
-# lib/onboard.sh — Onboard orchestration and PR migration
+# lib/onboard.sh — Unified onboard orchestration (reset + adopt strategies)
 #
 # Provides:
-#   onboard_flow()      — Interactive: import → wait for merge → reset to new repo
-#   migrate_one_pr()    — Migrate a single PR from archived repo to new repo
+#   onboard_flow()             — Interactive: import → wait → finalize
+#                                 finalize = subrepo_reset (rewrite) or
+#                                            adopt_branch (preserve)
+#   resolve_onboard_strategy() — Pick reset|adopt from --mode / config /
+#                                 ls-remote auto-detection
+#   migrate_one_pr()           — Migrate one PR from archived to new subrepo
 #
-# Onboard state is stored on the josh-sync-state branch at <target>/onboard.json.
-# Steps: start → importing → waiting-for-merge → resetting → complete
+# State is stored on the josh-sync-state branch at <target>/onboard.json:
+#   { step, strategy, import_prs, ... }
+# read_onboard_state falls back to legacy <target>/adopt.json (with implicit
+# strategy="adopt") so in-flight v2.1 adoptions continue to resume correctly.
 #
-# Requires: lib/core.sh, lib/config.sh, lib/auth.sh, lib/state.sh, lib/sync.sh sourced
-# Expects: JOSH_SYNC_TARGET_NAME, BOT_NAME, BOT_EMAIL, SUBREPO_API, SUBREPO_TOKEN, etc.
+# Steps:
+#   start → importing → waiting-for-merge → resetting | adopting → complete
+#
+# Requires: lib/core.sh, lib/config.sh, lib/auth.sh, lib/state.sh, lib/sync.sh,
+#           lib/adopt.sh sourced
+# Expects: JOSH_SYNC_TARGET_NAME, BOT_NAME, BOT_EMAIL, SUBREPO_API,
+#          SUBREPO_TOKEN, etc.
 
-# ─── Onboard State Helpers ────────────────────────────────────────
-# Follow the same pattern as read_state()/write_state() in lib/state.sh.
+# ─── State Helpers ────────────────────────────────────────────────
+# Same pattern as read_state()/write_state() in lib/state.sh.
 
 read_onboard_state() {
   local target_name="${1:-$JOSH_SYNC_TARGET_NAME}"
   git fetch origin "$STATE_BRANCH" 2>/dev/null || true
-  git show "origin/${STATE_BRANCH}:${target_name}/onboard.json" 2>/dev/null || echo '{}'
+
+  local json
+  json=$(git show "origin/${STATE_BRANCH}:${target_name}/onboard.json" 2>/dev/null || echo "")
+  if [ -n "$json" ]; then
+    # Pre-unification onboard.json had no .strategy field — the only flow that
+    # existed was the destructive reset path; treat missing/empty .strategy as
+    # reset so resume doesn't silently flip via re-resolution.
+    echo "$json" | jq '. + {strategy: ((.strategy // "") | if . == "" then "reset" else . end)}'
+    return
+  fi
+
+  # Backward-compat: fall back to v2.1 <target>/adopt.json so in-flight
+  # adoptions started before the unification continue to resume. The legacy
+  # schema lacks `.strategy`; inject "adopt" so resolve/dispatch downstream
+  # treats it correctly. Also drop the legacy `.mode` field (v2.1 carried it
+  # redundantly) to avoid future schema collisions.
+  json=$(git show "origin/${STATE_BRANCH}:${target_name}/adopt.json" 2>/dev/null || echo "")
+  if [ -n "$json" ]; then
+    echo "$json" | jq 'del(.mode) + {strategy: ((.strategy // "") | if . == "" then "adopt" else . end)}'
+    return
+  fi
+
+  echo '{}'
 }
 
 write_onboard_state() {
@@ -50,18 +83,97 @@ write_onboard_state() {
   git worktree remove "$tmp_dir" 2>/dev/null || rm -rf "$tmp_dir"
 }
 
+# Remove the v2.1 <target>/adopt.json from the state branch if present, so
+# that a --restart durably clears legacy state on the next read. Called by
+# onboard_flow's restart path.
+_onboard_state_remove_legacy() {
+  local target_name="${1:-$JOSH_SYNC_TARGET_NAME}"
+  git fetch origin "$STATE_BRANCH" 2>/dev/null || true
+  git show "origin/${STATE_BRANCH}:${target_name}/adopt.json" >/dev/null 2>&1 || return 0
+
+  local tmp_dir
+  tmp_dir=$(mktemp -d)
+  if ! git worktree add "$tmp_dir" "origin/${STATE_BRANCH}" 2>/dev/null; then
+    rm -rf "$tmp_dir"
+    return 0
+  fi
+  (
+    cd "$tmp_dir" || exit
+    git rm -q "${target_name}/adopt.json" 2>/dev/null || true
+    if ! git diff --cached --quiet 2>/dev/null; then
+      git -c user.name="$BOT_NAME" -c user.email="$BOT_EMAIL" \
+        commit -q -m "onboard: drop legacy ${target_name}/adopt.json on --restart"
+      git push -q origin "HEAD:${STATE_BRANCH}" || log "WARN" "Failed to push legacy adopt.json removal"
+    fi
+  )
+  git worktree remove "$tmp_dir" 2>/dev/null || rm -rf "$tmp_dir"
+}
+
+# ─── Strategy Resolution ──────────────────────────────────────────
+# Precedence (highest first):
+#   1. explicit --mode flag
+#   2. targets[].history_lock (preserve → adopt, rewrite → reset)
+#   3. auto-detect: subrepo has any branches → adopt, otherwise reset
+#
+# Prints the chosen strategy (reset|adopt) on stdout; logs the source on
+# stderr so the preflight line in cmd_onboard surfaces the choice.
+
+resolve_onboard_strategy() {
+  local target_json="$1"
+  local explicit_mode="${2:-}"
+
+  if [ -n "$explicit_mode" ]; then
+    case "$explicit_mode" in
+      reset|adopt) ;;
+      *) die "Invalid --mode '${explicit_mode}' (must be 'reset' or 'adopt')" ;;
+    esac
+    log "INFO" "Strategy: ${explicit_mode} (from --mode flag)"
+    echo "$explicit_mode"
+    return
+  fi
+
+  local history_lock
+  history_lock=$(echo "$target_json" | jq -r '.history_lock // empty')
+  if [ -n "$history_lock" ]; then
+    case "$history_lock" in
+      preserve)
+        log "INFO" "Strategy: adopt (from config history_lock: preserve)"
+        echo "adopt"; return ;;
+      rewrite)
+        log "INFO" "Strategy: reset (from config history_lock: rewrite)"
+        echo "reset"; return ;;
+      *)
+        die "Invalid history_lock '${history_lock}' in target config (must be 'preserve' or 'rewrite')" ;;
+    esac
+  fi
+
+  # Critical: distinguish a genuinely empty subrepo from a failed ls-remote.
+  # Treating an auth/network failure as "empty" would silently pick reset and
+  # force-push a live subrepo's history away.
+  local heads
+  if heads=$(git ls-remote --heads "$(subrepo_auth_url)" 2>/dev/null); then
+    if [ -n "$heads" ]; then
+      log "INFO" "Strategy: adopt (auto-detected — subrepo has branches)"
+      echo "adopt"
+    else
+      log "INFO" "Strategy: reset (auto-detected — subrepo has no branches)"
+      echo "reset"
+    fi
+  else
+    die "Cannot auto-detect strategy: 'git ls-remote' against the subrepo failed (auth/network). Pass --mode=reset|adopt explicitly, or set targets[].history_lock for this target."
+  fi
+}
+
 # ─── Derive Archived API URL ─────────────────────────────────────
 # Given a URL like "git@host:org/repo-archived.git" or
 # "https://host/org/repo-archived.git", derive the Gitea API URL.
 
 _archived_api_from_url() {
   local url="$1"
-  # Strip .git suffix first — avoids non-greedy regex issues in POSIX ERE
   url="${url%.git}"
   local host repo_path
 
   if echo "$url" | grep -qE '^(ssh://|git@)'; then
-    # SSH URL
     if echo "$url" | grep -q '^ssh://'; then
       host=$(echo "$url" | sed -E 's|ssh://[^@]*@([^/]+)/.*|\1|')
       repo_path=$(echo "$url" | sed -E 's|ssh://[^@]*@[^/]+/(.+)$|\1|')
@@ -70,7 +182,6 @@ _archived_api_from_url() {
       repo_path=$(echo "$url" | sed -E 's|git@[^:/]+[:/](.+)$|\1|')
     fi
   else
-    # HTTPS URL
     host=$(echo "$url" | sed -E 's|https?://([^/]+)/.*|\1|')
     repo_path=$(echo "$url" | sed -E 's|https?://[^/]+/(.+)$|\1|')
   fi
@@ -80,38 +191,57 @@ _archived_api_from_url() {
 
 # ─── Onboard Flow ────────────────────────────────────────────────
 # Interactive orchestrator with checkpoint/resume.
-# Usage: onboard_flow <target_json> <restart>
+# Usage: onboard_flow <target_json> <restart> [explicit_mode]
+#   explicit_mode — "reset", "adopt", or "" for auto-resolve.
 
 onboard_flow() {
   local target_json="$1"
   local restart="${2:-false}"
+  local explicit_mode="${3:-}"
   local target_name="$JOSH_SYNC_TARGET_NAME"
 
-  # Load existing onboard state (or empty)
-  local onboard_state
-  onboard_state=$(read_onboard_state "$target_name")
-  local current_step
-  current_step=$(echo "$onboard_state" | jq -r '.step // "start"')
+  local state current_step strategy
+  state=$(read_onboard_state "$target_name")
+  current_step=$(echo "$state" | jq -r '.step // "start"')
+  strategy=$(echo "$state" | jq -r '.strategy // empty')
 
   if [ "$restart" = true ]; then
     log "INFO" "Restarting onboard from scratch"
     current_step="start"
-    onboard_state='{}'
+    state='{}'
+    strategy=""
+    # Durably clear any legacy v2.1 adopt.json so the next read doesn't
+    # silently fall back to it.
+    _onboard_state_remove_legacy "$target_name"
   fi
 
+  if [ -z "$strategy" ]; then
+    strategy=$(resolve_onboard_strategy "$target_json" "$explicit_mode")
+  elif [ -n "$explicit_mode" ] && [ "$strategy" != "$explicit_mode" ]; then
+    die "Saved strategy is '${strategy}' (mid-flow); cannot switch to --mode=${explicit_mode} without --restart."
+  else
+    log "INFO" "Strategy: ${strategy} (resumed from state)"
+  fi
+
+  case "$strategy" in
+    reset|adopt) ;;
+    *) die "Unknown strategy '${strategy}' in state (corrupt?). Re-run with --restart to start over." ;;
+  esac
+
   log "INFO" "Onboard step: ${current_step}"
 
-  # ── Step 1: Prerequisites + archived repo info ──
+  # ── Step 1: Strategy-specific intro and (for reset) archived repo info ──
   if [ "$current_step" = "start" ]; then
     echo "" >&2
-    echo "=== Onboarding ${target_name} ===" >&2
+    echo "=== Onboarding ${target_name} (strategy: ${strategy}) ===" >&2
     echo "" >&2
+
+    if [ "$strategy" = "reset" ]; then
       echo "Before proceeding, you should have:" >&2
       echo "  1. Renamed the existing subrepo (e.g., storefront → storefront-archived)" >&2
       echo "  2. Created a new EMPTY repo at the original URL" >&2
       echo "" >&2
 
-    # Verify the new (empty) subrepo is reachable (no HEAD ref — works on empty repos)
       if git ls-remote "$(subrepo_auth_url)" >/dev/null 2>&1; then
         # shellcheck disable=SC2001  # sed is clearer for URL pattern replacement
         log "INFO" "New subrepo is reachable at $(echo "$SUBREPO_URL" | sed 's|://[^@]*@|://***@|')"
@@ -124,14 +254,10 @@ onboard_flow() {
       read -r archived_url
       [ -n "$archived_url" ] || die "Archived URL is required"
 
-    # Determine auth type for archived repo (same as current subrepo)
       local archived_auth="${SUBREPO_AUTH:-https}"
-
-    # Derive API URL
       local archived_api
       archived_api=$(_archived_api_from_url "$archived_url")
 
-    # Verify archived repo is reachable via API
       if curl -sf -H "Authorization: token ${SUBREPO_TOKEN}" \
         "${archived_api}" >/dev/null 2>&1; then
         log "INFO" "Archived repo reachable: ${archived_api}"
@@ -143,49 +269,60 @@ onboard_flow() {
         [ "$confirm" = "y" ] || [ "$confirm" = "Y" ] || die "Aborted"
       fi
 
-    # Save state
-    onboard_state=$(jq -n \
+      state=$(jq -n \
         --arg step "importing" \
+        --arg strategy "reset" \
         --arg archived_api "$archived_api" \
         --arg archived_url "$archived_url" \
         --arg archived_auth "$archived_auth" \
         --arg ts "$(date -u +%Y-%m-%dT%H:%M:%SZ)" \
-      '{step:$step, archived_api:$archived_api, archived_url:$archived_url,
-        archived_auth:$archived_auth, import_prs:{}, reset_branches:[],
-        migrated_prs:[], timestamp:$ts}')
-    write_onboard_state "$target_name" "$onboard_state"
+        '{step:$step, strategy:$strategy, archived_api:$archived_api,
+          archived_url:$archived_url, archived_auth:$archived_auth,
+          import_prs:{}, reset_branches:[], migrated_prs:[], timestamp:$ts}')
+    else
+      # strategy = adopt
+      echo "This keeps the existing subrepo history and adds one adoption merge commit per branch." >&2
+      echo "No force-push is used. Existing open PR branches remain based on the old history." >&2
+      echo "" >&2
+
+      state=$(jq -n \
+        --arg step "importing" \
+        --arg strategy "adopt" \
+        --arg ts "$(date -u +%Y-%m-%dT%H:%M:%SZ)" \
+        '{step:$step, strategy:$strategy, import_prs:{}, adopted_branches:[], timestamp:$ts}')
+    fi
+
+    write_onboard_state "$target_name" "$state"
     current_step="importing"
   fi
 
-  # ── Step 2: Import (reuses initial_import()) ──
+  # ── Step 2: Import (reset uses archived clone URL; adopt uses subrepo URL) ──
   if [ "$current_step" = "importing" ]; then
     echo "" >&2
     log "INFO" "Step 2: Importing subrepo content into monorepo..."
 
-    local branches
+    local branches import_prs
     branches=$(echo "$target_json" | jq -r '.branches | keys[]')
+    import_prs=$(echo "$state" | jq -r '.import_prs // {}')
 
-    # Load existing import_prs from state (resume support)
-    local import_prs
-    import_prs=$(echo "$onboard_state" | jq -r '.import_prs // {}')
-
-    # Build the archived repo clone URL for initial_import().
-    # The content lives in the archived repo — the new repo at SUBREPO_URL is empty.
-    local archived_url archived_clone_url
-    archived_url=$(echo "$onboard_state" | jq -r '.archived_url')
+    local archived_clone_url=""
+    if [ "$strategy" = "reset" ]; then
+      local archived_url
+      archived_url=$(echo "$state" | jq -r '.archived_url // empty')
+      [ -n "$archived_url" ] || die "Reset strategy: archived_url missing from state (corrupt or interrupted before start step finished). Re-run with --restart."
       if [ "${SUBREPO_AUTH:-https}" = "ssh" ]; then
         archived_clone_url="$archived_url"
       else
         # shellcheck disable=SC2001
         archived_clone_url=$(echo "$archived_url" | sed "s|https://|https://${BOT_USER}:${SUBREPO_TOKEN}@|")
       fi
+    fi
 
     for branch in $branches; do
       local mapped
       mapped=$(echo "$target_json" | jq -r --arg b "$branch" '.branches[$b] // empty')
       [ -z "$mapped" ] && continue
 
-      # Skip branches that already have an import PR recorded
       if echo "$import_prs" | jq -e --arg b "$branch" 'has($b)' >/dev/null 2>&1; then
         log "INFO" "Import PR already recorded for ${branch} — skipping"
         continue
@@ -196,11 +333,14 @@ onboard_flow() {
 
       log "INFO" "Importing branch: ${branch} (subrepo: ${mapped})"
       local result
+      if [ -n "$archived_clone_url" ]; then
         result=$(initial_import "$archived_clone_url")
+      else
+        result=$(initial_import)
+      fi
       log "INFO" "Import result for ${branch}: ${result}"
 
       if [ "$result" = "pr-created" ]; then
-        # Find the import PR number via API
         local prs pr_number
         prs=$(list_open_prs "$MONOREPO_API" "$GITEA_TOKEN")
         pr_number=$(echo "$prs" | jq -r --arg t "$target_name" --arg b "$branch" \
@@ -210,37 +350,35 @@ onboard_flow() {
           import_prs=$(echo "$import_prs" | jq --arg b "$branch" --arg n "$pr_number" '. + {($b): ($n | tonumber)}')
           log "INFO" "Import PR for ${branch}: #${pr_number}"
         else
-          log "WARN" "Could not find import PR number for ${branch} — check monorepo PRs"
+          # Same hazard for both strategies: continuing without recording the
+          # PR number means the next resume re-runs initial_import and creates
+          # a duplicate import PR. Bail out and let the user reconcile.
+          die "Could not find import PR number for ${branch} on monorepo. Re-running would create a duplicate import PR — check the monorepo's open PRs first."
         fi
       fi
 
-      # Save progress after each branch (resume support)
-      onboard_state=$(echo "$onboard_state" | jq --argjson prs "$import_prs" '.import_prs = $prs')
-      write_onboard_state "$target_name" "$onboard_state"
+      state=$(echo "$state" | jq --argjson prs "$import_prs" '.import_prs = $prs')
+      write_onboard_state "$target_name" "$state"
     done
 
-    # Update state
-    onboard_state=$(echo "$onboard_state" | jq \
+    state=$(echo "$state" | jq \
       --arg step "waiting-for-merge" \
       --argjson prs "$import_prs" \
       '.step = $step | .import_prs = $prs')
-    write_onboard_state "$target_name" "$onboard_state"
+    write_onboard_state "$target_name" "$state"
     current_step="waiting-for-merge"
   fi
 
-  # ── Step 3: Wait for merge ──
+  # ── Step 3: Wait for import PR(s) to merge ──
   if [ "$current_step" = "waiting-for-merge" ]; then
     echo "" >&2
     log "INFO" "Step 3: Waiting for import PR(s) to be merged..."
 
-    local import_prs
-    import_prs=$(echo "$onboard_state" | jq -r '.import_prs')
-    local pr_count
+    local import_prs pr_count
+    import_prs=$(echo "$state" | jq -r '.import_prs')
     pr_count=$(echo "$import_prs" | jq 'length')
 
-    if [ "$pr_count" -eq 0 ]; then
-      log "WARN" "No import PRs recorded — skipping merge check"
-    else
+    if [ "$pr_count" -gt 0 ]; then
       echo "" >&2
       echo "Import PRs to merge:" >&2
       echo "$import_prs" | jq -r 'to_entries[] | "  \(.key): PR #\(.value)"' >&2
@@ -248,12 +386,10 @@ onboard_flow() {
       echo "Merge the import PR(s) on the monorepo, then press Enter..." >&2
       read -r
 
-      # Verify each PR is merged
       local all_merged=true
       for branch in $(echo "$import_prs" | jq -r 'keys[]'); do
-        local pr_number
+        local pr_number pr_json merged
         pr_number=$(echo "$import_prs" | jq -r --arg b "$branch" '.[$b]')
-        local pr_json merged
         pr_json=$(get_pr "$MONOREPO_API" "$GITEA_TOKEN" "$pr_number")
         merged=$(echo "$pr_json" | jq -r '.merged // false')
 
@@ -268,26 +404,31 @@ onboard_flow() {
       if [ "$all_merged" = false ]; then
         die "Not all import PRs are merged. Re-run 'josh-sync onboard ${target_name}' after merging."
       fi
+    else
+      log "INFO" "No import PRs recorded — subfolder already matched subrepo"
     fi
 
-    # Update state
-    onboard_state=$(echo "$onboard_state" | jq '.step = "resetting"')
-    write_onboard_state "$target_name" "$onboard_state"
-    current_step="resetting"
+    local next_step
+    if [ "$strategy" = "reset" ]; then
+      next_step="resetting"
+    else
+      next_step="adopting"
+    fi
+    state=$(echo "$state" | jq --arg s "$next_step" '.step = $s')
+    write_onboard_state "$target_name" "$state"
+    current_step="$next_step"
   fi
 
-  # ── Step 4: Reset (pushes josh-filtered history to new repo) ──
+  # ── Step 4a: Finalize via reset (force-push josh-filtered history) ──
   if [ "$current_step" = "resetting" ]; then
     echo "" >&2
     log "INFO" "Step 4: Pushing josh-filtered history to new subrepo..."
 
-    local branches
+    local branches already_reset
     branches=$(echo "$target_json" | jq -r '.branches | keys[]')
-    local already_reset
-    already_reset=$(echo "$onboard_state" | jq -r '.reset_branches // []')
+    already_reset=$(echo "$state" | jq -r '.reset_branches // []')
 
     for branch in $branches; do
-      # Skip branches already reset (resume support)
       if echo "$already_reset" | jq -e --arg b "$branch" 'index($b) != null' >/dev/null 2>&1; then
         log "INFO" "Branch ${branch} already reset — skipping"
         continue
@@ -304,18 +445,69 @@ onboard_flow() {
       result=$(subrepo_reset)
       log "INFO" "Reset result for ${branch}: ${result}"
 
-      # Track progress
-      onboard_state=$(echo "$onboard_state" | jq --arg b "$branch" \
-        '.reset_branches += [$b]')
-      write_onboard_state "$target_name" "$onboard_state"
+      state=$(echo "$state" | jq --arg b "$branch" '.reset_branches += [$b]')
+      write_onboard_state "$target_name" "$state"
     done
 
-    # Update state
-    onboard_state=$(echo "$onboard_state" | jq \
+    state=$(echo "$state" | jq \
       --arg step "complete" \
       --arg ts "$(date -u +%Y-%m-%dT%H:%M:%SZ)" \
       '.step = $step | .timestamp = $ts')
-    write_onboard_state "$target_name" "$onboard_state"
+    write_onboard_state "$target_name" "$state"
+    current_step="complete"
+  fi
+
+  # ── Step 4b: Finalize via adoption merge ──
+  if [ "$current_step" = "adopting" ]; then
+    echo "" >&2
+    log "INFO" "Step 4: Creating adoption merge commit(s)..."
+
+    local branches already_adopted
+    branches=$(echo "$target_json" | jq -r '.branches | keys[]')
+    already_adopted=$(echo "$state" | jq -r '.adopted_branches // []')
+
+    for branch in $branches; do
+      if echo "$already_adopted" | jq -e --arg b "$branch" 'index($b) != null' >/dev/null 2>&1; then
+        log "INFO" "Branch ${branch} already adopted — skipping"
+        continue
+      fi
+
+      local mapped
+      mapped=$(echo "$target_json" | jq -r --arg b "$branch" '.branches[$b] // empty')
+      [ -z "$mapped" ] && continue
+
+      export SYNC_BRANCH_MONO="$branch"
+      export SYNC_BRANCH_SUBREPO="$mapped"
+
+      local result
+      result=$(adopt_branch)
+      log "INFO" "Adopt result for ${branch}: ${result}"
+
+      case "$result" in
+        adopted|already-adopted)
+          state=$(echo "$state" | jq --arg b "$branch" '.adopted_branches += [$b]')
+          write_onboard_state "$target_name" "$state"
+          ;;
+        tree-mismatch)
+          die "Tree mismatch for ${branch}. Merge the import PR and make sure subrepo/${mapped} matches the Josh-filtered monorepo tree."
+          ;;
+        push-rejected)
+          die "Subrepo branch ${mapped} changed during adoption. Re-run 'josh-sync onboard ${target_name} --mode=adopt' to retry."
+          ;;
+        missing-branch)
+          die "Subrepo branch ${mapped} does not exist."
+          ;;
+        *)
+          die "Unexpected adopt result: ${result}"
+          ;;
+      esac
+    done
+
+    state=$(echo "$state" | jq \
+      --arg step "complete" \
+      --arg ts "$(date -u +%Y-%m-%dT%H:%M:%SZ)" \
+      '.step = $step | .timestamp = $ts')
+    write_onboard_state "$target_name" "$state"
     current_step="complete"
   fi
 
@@ -324,6 +516,7 @@ onboard_flow() {
     echo "" >&2
     echo "=== Onboarding complete! ===" >&2
     echo "" >&2
+    if [ "$strategy" = "reset" ]; then
       echo "The new subrepo now has josh-filtered history." >&2
       echo "Developers should re-clone or reset their local copies:" >&2
       echo "  git fetch origin && git reset --hard origin/main" >&2
@@ -332,6 +525,11 @@ onboard_flow() {
       echo "  josh-sync migrate-pr ${target_name}        # interactive picker" >&2
       echo "  josh-sync migrate-pr ${target_name} --all   # migrate all" >&2
       echo "  josh-sync migrate-pr ${target_name} 5 8 12  # specific PRs" >&2
+    else
+      echo "The subrepo keeps its existing history and now has a josh-sync adoption merge." >&2
+      echo "Developers can keep their clones; they only need to fast-forward active branches:" >&2
+      echo "  git fetch origin && git checkout main && git merge --ff-only origin/main" >&2
+    fi
   fi
 }
 
@@ -346,15 +544,17 @@ migrate_one_pr() {
   local pr_number="$1"
   local target_name="$JOSH_SYNC_TARGET_NAME"
 
-  # Read archived repo info from onboard state
-  local onboard_state archived_api
+  local onboard_state strategy archived_api
   onboard_state=$(read_onboard_state "$target_name")
+  strategy=$(echo "$onboard_state" | jq -r '.strategy // "reset"')
+  if [ "$strategy" = "adopt" ]; then
+    die "Target '${target_name}' was onboarded with the adopt strategy, which does not record an archived repo. migrate-pr only applies to the reset strategy."
+  fi
   archived_api=$(echo "$onboard_state" | jq -r '.archived_api')
   if [ -z "$archived_api" ] || [ "$archived_api" = "null" ]; then
-    die "No archived repo info found. Run 'josh-sync onboard ${target_name}' first."
+    die "No archived repo info found for '${target_name}'. Run 'josh-sync onboard ${target_name} --mode=reset' first."
   fi
 
-  # Check if this PR was already migrated
   local already_migrated
   already_migrated=$(echo "$onboard_state" | jq -r \
     --argjson num "$pr_number" '.migrated_prs // [] | map(select(.old_number == $num)) | length')
@@ -363,10 +563,8 @@ migrate_one_pr() {
     return 0
   fi
 
-  # Same credentials — the repo was just renamed
   local archived_token="$SUBREPO_TOKEN"
 
-  # 1. Get PR metadata from archived repo
   local pr_json title base head body
   pr_json=$(get_pr "$archived_api" "$archived_token" "$pr_number") \
     || die "Failed to fetch PR #${pr_number} from archived repo"
@@ -377,8 +575,6 @@ migrate_one_pr() {
 
   log "INFO" "Migrating PR #${pr_number}: \"${title}\" (${base} <- ${head})"
 
-  # 2. Clone new subrepo, add archived repo as second remote
-  # Save cwd so we can restore it (function runs in caller's shell, not subshell)
   local original_dir
   original_dir=$(pwd)
 
@@ -394,7 +590,6 @@ migrate_one_pr() {
   git config user.name "$BOT_NAME"
   git config user.email "$BOT_EMAIL"
 
-  # Build authenticated URL for the archived repo
   local archived_url archived_clone_url
   archived_url=$(echo "$onboard_state" | jq -r '.archived_url')
   if [ "${SUBREPO_AUTH:-https}" = "ssh" ]; then
@@ -404,12 +599,10 @@ migrate_one_pr() {
     archived_clone_url=$(echo "$archived_url" | sed "s|https://|https://${BOT_USER}:${SUBREPO_TOKEN}@|")
   fi
 
-  # Fetch the PR's head and base branches from the archived repo
   git remote add archived "$archived_clone_url"
   git fetch archived "$head" "$base" 2>&1 \
     || die "Failed to fetch branches from archived repo"
 
-  # 3. Compute diff locally and apply with --3way
   git checkout -B "$head" >&2
 
   local diff
@@ -428,13 +621,11 @@ Migrated from archived repo PR #${pr_number}" >&2
     git push "$(subrepo_auth_url)" "$head" >&2 \
       || die "Failed to push branch ${head}"
 
-    # 4. Create PR on new repo
     local new_number
     new_number=$(create_pr_number "$SUBREPO_API" "$SUBREPO_TOKEN" \
       "$base" "$head" "$title" "$body")
     log "INFO" "Migrated PR #${pr_number} -> #${new_number}: \"${title}\""
 
-    # 5. Record in onboard state
     cd "$original_dir" || true
     onboard_state=$(read_onboard_state "$target_name")
     onboard_state=$(echo "$onboard_state" | jq \

lib/sync.sh

@@ -11,7 +11,7 @@
 
 # ─── Forward Sync: Monorepo → Subrepo ──────────────────────────────
 #
-# Returns: fresh | skip | clean | lease-rejected | conflict
+# Returns: fresh | skip | clean | lease-rejected | conflict | unrelated
 
 forward_sync() {
   local mono_branch="$SYNC_BRANCH_MONO"
@@ -97,7 +97,14 @@ ${BOT_TRAILER}: forward/${mono_branch}/$(date -u +%Y-%m-%dT%H:%M:%SZ)" >&2
     fi
 
   else
-    # Conflict!
+    # Check: unrelated histories (filter change) vs normal merge conflict
+    if ! git merge-base "subrepo/${subrepo_branch}" "$mono_head" >/dev/null 2>&1; then
+      log "INFO" "No common ancestor — histories are unrelated (filter change?)"
+      echo "unrelated"
+      return
+    fi
+
+    # Normal merge conflict
     local conflicted
     conflicted=$(git diff --name-only --diff-filter=U 2>/dev/null || echo "(unknown)")
     git merge --abort
@@ -115,7 +122,14 @@ ${BOT_TRAILER}: forward/${mono_branch}/$(date -u +%Y-%m-%dT%H:%M:%SZ)" >&2
     local pr_body conflicted_list
     # shellcheck disable=SC2001
     conflicted_list=$(echo "$conflicted" | sed 's/^/- /')
-    pr_body="## Sync Conflict\n\nMonorepo \`${mono_branch}\` has changes that conflict with \`${subrepo_branch}\`.\n\n**Conflicted files:**\n${conflicted_list}\n\nPlease resolve and merge this PR to complete the sync."
+    pr_body="## Sync Conflict
+
+Monorepo \`${mono_branch}\` has changes that conflict with \`${subrepo_branch}\`.
+
+**Conflicted files:**
+${conflicted_list}
+
+Please resolve and merge this PR to complete the sync."
 
     create_pr "${SUBREPO_API}" "${SUBREPO_TOKEN}" \
       "$subrepo_branch" "$conflict_branch" \
@@ -128,10 +142,93 @@ ${BOT_TRAILER}: forward/${mono_branch}/$(date -u +%Y-%m-%dT%H:%M:%SZ)" >&2
   fi
 }
 
+# ─── Filter Change Reconciliation ─────────────────────────────────
+# When the josh filter changes (e.g., exclude patterns added/removed),
+# josh-proxy recomputes filtered history with new SHAs. This creates a
+# merge commit on the subrepo that connects old and new histories,
+# re-establishing shared ancestry without a destructive force-push.
+# Returns: reconciled | lease-rejected
+
+reconcile_filter_change() {
+  local mono_branch="$SYNC_BRANCH_MONO"
+  local subrepo_branch="$SYNC_BRANCH_SUBREPO"
+  local work_dir
+  work_dir=$(mktemp -d)
+  # shellcheck disable=SC2064  # Intentional early expansion — work_dir is local
+  trap "rm -rf '$work_dir'" EXIT
+
+  log "INFO" "=== Filter change reconciliation: ${mono_branch} ==="
+
+  # 1. Clone subrepo
+  git clone "$(subrepo_auth_url)" \
+    --branch "$subrepo_branch" --single-branch \
+    "${work_dir}/subrepo" || die "Failed to clone subrepo"
+
+  cd "${work_dir}/subrepo" || exit
+  git config user.name "$BOT_NAME"
+  git config user.email "$BOT_EMAIL"
+
+  local subrepo_head
+  subrepo_head=$(git rev-parse HEAD)
+  log "INFO" "Subrepo HEAD: ${subrepo_head:0:12}"
+
+  # 2. Fetch josh-proxy filtered view (new filter)
+  git remote add josh-filtered "$(josh_auth_url)"
+  git fetch josh-filtered "$mono_branch" || die "Failed to fetch from josh-proxy"
+
+  local josh_head josh_tree
+  josh_head=$(git rev-parse "josh-filtered/${mono_branch}")
+  # shellcheck disable=SC1083  # {tree} is git syntax, not shell brace expansion
+  josh_tree=$(git rev-parse "josh-filtered/${mono_branch}^{tree}")
+  log "INFO" "Josh-proxy HEAD (new filter): ${josh_head:0:12}"
+
+  # 3. Check if trees are already identical (filter change had no effect)
+  local subrepo_tree
+  # shellcheck disable=SC1083
+  subrepo_tree=$(git rev-parse "HEAD^{tree}")
+  if [ "$josh_tree" = "$subrepo_tree" ]; then
+    log "INFO" "Trees identical after filter change — no reconciliation needed"
+    echo "skip"
+    return
+  fi
+
+  # 4. Create merge commit: josh-proxy HEAD (first parent) + subrepo HEAD, with josh-proxy's tree
+  # Josh follows first-parent traversal — josh-filtered MUST be first so josh can map
+  # the history back to the monorepo. Old subrepo history hangs off parent 2.
+  local merge_commit
+  merge_commit=$(git commit-tree "$josh_tree" \
+    -p "$josh_head" \
+    -p "$subrepo_head" \
+    -m "Sync: filter configuration updated
+
+${BOT_TRAILER}: filter-change/${mono_branch}/$(date -u +%Y-%m-%dT%H:%M:%SZ)")
+
+  git reset --hard "$merge_commit" >&2
+  log "INFO" "Created reconciliation merge: ${merge_commit:0:12}"
+
+  # 5. Record lease and push
+  local subrepo_sha
+  subrepo_sha=$(subrepo_ls_remote "$subrepo_branch")
+
+  if git push \
+    --force-with-lease="refs/heads/${subrepo_branch}:${subrepo_sha}" \
+    "$(subrepo_auth_url)" \
+    "HEAD:refs/heads/${subrepo_branch}"; then
+
+    log "INFO" "Filter change reconciled — shared ancestry re-established"
+    echo "reconciled"
+  else
+    log "WARN" "Force-with-lease rejected — subrepo changed during reconciliation"
+    echo "lease-rejected"
+  fi
+}
+
 # ─── Reverse Sync: Subrepo → Monorepo ──────────────────────────────
 #
 # Always creates a PR on the monorepo — never pushes directly.
-# Returns: skip | pr-created | josh-rejected
+# Returns: skip | skip-dirty | pr-created | josh-rejected
+#   skip       — trees identical, nothing to do
+#   skip-dirty — trees differ but no human commits found (don't update state)
 
 reverse_sync() {
   local mono_branch="$SYNC_BRANCH_MONO"
@@ -143,6 +240,8 @@ reverse_sync() {
 
   log "INFO" "=== Reverse sync: subrepo/${subrepo_branch} → mono/${mono_branch} ==="
 
+  local force_mode="${SYNC_REVERSE_FORCE:-0}"
+
   # 1. Clone subrepo
   git clone "$(subrepo_auth_url)" \
     --branch "$subrepo_branch" --single-branch \
@@ -156,31 +255,190 @@ reverse_sync() {
   git remote add mono-filtered "$(josh_auth_url)"
   git fetch mono-filtered "$mono_branch" || die "Failed to fetch from josh-proxy"
 
-  # 3. Find new human commits (excludes bot commits from forward sync)
-  local human_commits
-  human_commits=$(git log "mono-filtered/${mono_branch}..HEAD" \
-    --oneline --invert-grep --grep="^${BOT_TRAILER}:" 2>/dev/null || echo "")
+  # 3. Compare trees — skip if subrepo matches josh-filtered view
+  local subrepo_tree josh_tree
+  # shellcheck disable=SC1083  # {tree} is git syntax, not shell brace expansion
+  subrepo_tree=$(git rev-parse "HEAD^{tree}")
+  # shellcheck disable=SC1083
+  josh_tree=$(git rev-parse "mono-filtered/${mono_branch}^{tree}")
 
-  if [ -z "$human_commits" ]; then
-    log "INFO" "No new human commits in subrepo — nothing to sync"
+  if [ "$subrepo_tree" = "$josh_tree" ]; then
+    log "INFO" "Subrepo tree matches josh-filtered view — nothing to sync"
     echo "skip"
     return
   fi
 
+  # 4. Find new human commits (excludes bot commits from forward sync)
+  #    Uses merge-base + --ancestry-path to restrict to the direct lineage.
+  #    merge-base is needed because mono-filtered may have advanced past the
+  #    last forward sync (any monorepo commit, even outside the subfolder,
+  #    causes josh to create a new filtered commit).  Using mono-filtered
+  #    directly with --ancestry-path returns empty when it's not an ancestor
+  #    of HEAD.  merge-base always finds the last connected point.
+  local base human_commits
+  base=$(git merge-base "mono-filtered/${mono_branch}" HEAD 2>/dev/null || echo "")
+
+  if [ -n "$base" ]; then
+    human_commits=$(git log --ancestry-path "${base}..HEAD" \
+      --oneline --invert-grep --grep="^${BOT_TRAILER}:" 2>/dev/null || echo "")
+  else
+    # No common ancestor (first sync or fully diverged) — skip ancestry-path
+    human_commits=$(git log "mono-filtered/${mono_branch}..HEAD" \
+      --oneline --invert-grep --grep="^${BOT_TRAILER}:" 2>/dev/null || echo "")
+  fi
+
+  if [ -z "$human_commits" ]; then
+    if [ "$force_mode" = "1" ]; then
+      log "WARN" "No human commits found — force mode: continuing anyway"
+    else
+      log "INFO" "No new human commits in subrepo — nothing to sync"
+      echo "skip-dirty"
+      return
+    fi
+  fi
+
   log "INFO" "New human commits to sync:"
   echo "$human_commits" >&2
 
-  # 4. Push through josh to a staging branch
+  # 5. Push through josh to a staging branch
   local ts
   ts=$(date +%Y%m%d-%H%M%S)
   local staging_branch="auto-sync/subrepo-${subrepo_branch}-${ts}"
+  local push_ref="HEAD"
+  local linearized=false
 
-  if git push -o "base=${mono_branch}" "$(josh_auth_url)" "HEAD:refs/heads/${staging_branch}"; then
-    log "INFO" "Pushed to staging branch via josh: ${staging_branch}"
+  if ! git push -o "base=${mono_branch}" "$(josh_auth_url)" "${push_ref}:refs/heads/${staging_branch}" 2>/dev/null; then
+    # Josh rejects pushes when the history contains merge commits whose
+    # parents it cannot map (e.g., merges of staging/feature branches that
+    # include auto-sync history).  Fall back to linearizing: cherry-pick
+    # regular commits as-is, squash only the problematic merge commits.
+    # See ADR-011.
+    log "WARN" "Direct push failed — linearizing history (cherry-pick + squash merges)"
+    log "INFO" "─── linearize start ───"
 
-    # 5. Create PR on monorepo (NEVER direct push)
+    local original_head
+    original_head=$(git rev-parse HEAD)
+
+    git checkout -b "tmp-linearize-$$" "mono-filtered/${mono_branch}" >/dev/null 2>&1 \
+      || die "Failed to create linearize branch"
+
+    # Reuse merge-base from step 4 (same reasoning: mono-filtered may have
+    # advanced past the last forward sync, breaking --ancestry-path).
+    local commit_shas
+    if [ -n "$base" ]; then
+      commit_shas=$(git log --ancestry-path "${base}..${original_head}" \
+        --reverse --format="%H" --invert-grep --grep="^${BOT_TRAILER}:" 2>/dev/null || echo "")
+    else
+      commit_shas=$(git log "mono-filtered/${mono_branch}..${original_head}" \
+        --reverse --format="%H" --invert-grep --grep="^${BOT_TRAILER}:" 2>/dev/null || echo "")
+    fi
+
+    local sha
+    for sha in $commit_shas; do
+      local parent_count
+      parent_count=$(git cat-file -p "$sha" | grep -c "^parent ")
+      local short_msg
+      short_msg=$(git log -1 --format="%s" "$sha")
+
+      if [ "$parent_count" -le 1 ]; then
+        # Regular commit — cherry-pick to preserve message and authorship
+        if git cherry-pick "$sha" >/dev/null 2>&1; then
+          log "INFO" "  cherry-pick ${sha:0:7}: ${short_msg}"
+        else
+          log "WARN" "  conflict ${sha:0:7} — applying patch from parent"
+          git cherry-pick --abort 2>/dev/null
+          local msg author_name author_email author_date
+          msg=$(git log -1 --format="%B" "$sha")
+          author_name=$(git log -1 --format="%an" "$sha")
+          author_email=$(git log -1 --format="%ae" "$sha")
+          author_date=$(git log -1 --format="%aI" "$sha")
+          # Diff from the commit's own parent — NOT from HEAD (which is
+          # the linearize branch and may have a different base).
+          git diff "${sha}^" "$sha" | git apply --index >/dev/null 2>&1 \
+            || die "Failed to apply diff for ${sha:0:7}"
+          GIT_AUTHOR_NAME="$author_name" GIT_AUTHOR_EMAIL="$author_email" \
+            GIT_AUTHOR_DATE="$author_date" \
+            git commit -m "$msg" >/dev/null 2>&1 || die "Failed to commit ${sha:0:7}"
+          log "INFO" "  applied   ${sha:0:7}: ${short_msg}"
+        fi
+      else
+        # Merge commit — cherry-pick relative to first parent (squashes the merge)
+        local msg author_name author_email author_date
+        msg=$(git log -1 --format="%B" "$sha")
+        author_name=$(git log -1 --format="%an" "$sha")
+        author_email=$(git log -1 --format="%ae" "$sha")
+        author_date=$(git log -1 --format="%aI" "$sha")
+
+        if git cherry-pick -m 1 "$sha" >/dev/null 2>&1; then
+          log "INFO" "  squash    ${sha:0:7}: ${short_msg}"
+        else
+          # Cherry-pick failed — distinguish empty result (changes already
+          # applied by a prior cherry-pick) from a real conflict.
+          if git diff --cached --quiet 2>/dev/null && git diff --quiet 2>/dev/null; then
+            # Working tree clean — the merge changes are already present
+            git cherry-pick --abort 2>/dev/null || git reset --hard HEAD >/dev/null 2>&1
+            log "INFO" "  skip      ${sha:0:7}: ${short_msg} (already applied)"
+          else
+            # Real conflict — apply diff from first parent (what the merge
+            # actually introduced, NOT from HEAD which would capture all
+            # tree differences).
+            git cherry-pick --abort 2>/dev/null
+            git diff "${sha}^1" "$sha" | git apply --index >/dev/null 2>&1 \
+              || die "Failed to apply merge diff for ${sha:0:7}"
+            GIT_AUTHOR_NAME="$author_name" GIT_AUTHOR_EMAIL="$author_email" \
+              GIT_AUTHOR_DATE="$author_date" \
+              git commit -m "$msg" >/dev/null 2>&1 || die "Failed to commit merge ${sha:0:7}"
+            log "INFO" "  squash    ${sha:0:7}: ${short_msg}"
+          fi
+        fi
+      fi
+    done
+
+    log "INFO" "─── linearize done ────"
+
+    push_ref="HEAD"
+    linearized=true
+
+    git push -o "base=${mono_branch}" "$(josh_auth_url)" \
+      "${push_ref}:refs/heads/${staging_branch}" \
+      || { log "ERROR" "Josh rejected linearized push — check josh-proxy logs"; echo "josh-rejected"; return; }
+  fi
+
+  log "INFO" "Pushed to staging branch via josh: ${staging_branch}${linearized:+ (linearized)}"
+
+  # 6. Publish: force-push directly (--force) or create PR (default)
+  if [ "$force_mode" = "1" ]; then
+    log "WARN" "Force mode: pushing ${staging_branch} directly to mono/${mono_branch} — bypassing PR"
+    local mono_dir="${work_dir}/monorepo"
+    git clone "$(mono_auth_url)" \
+      --branch "$staging_branch" --single-branch \
+      "$mono_dir" || die "Failed to clone monorepo staging branch for force-push"
+    git -C "$mono_dir" push --force "$(mono_auth_url)" \
+      "HEAD:refs/heads/${mono_branch}" \
+      || die "Failed to force-push to mono/${mono_branch}"
+    log "INFO" "Force-pushed mono/${staging_branch} → mono/${mono_branch}"
+    echo "forced"
+  else
     local pr_body
-    pr_body="## Subrepo changes\n\nNew commits from subrepo \`${subrepo_branch}\`:\n\n\`\`\`\n${human_commits}\n\`\`\`\n\n**Review checklist:**\n- [ ] Changes scoped to synced subfolder\n- [ ] No leaked credentials or environment-specific config\n- [ ] CI passes"
+    local linearize_note=""
+    if [ "$linearized" = true ]; then
+      linearize_note="
+> **Note:** Merge commits were squashed during sync because the subrepo
+> history contained merges that josh-proxy cannot map (see ADR-011).
+> Regular commits are preserved individually."
+    fi
+    pr_body="## Subrepo changes
+
+New commits from subrepo \`${subrepo_branch}\`:
+
+\`\`\`
+${human_commits}
+\`\`\`
+${linearize_note}
+**Review checklist:**
+- [ ] Changes scoped to synced subfolder
+- [ ] No leaked credentials or environment-specific config
+- [ ] CI passes"
 
     create_pr "${MONOREPO_API}" "${GITEA_TOKEN}" \
       "$mono_branch" "$staging_branch" \
@@ -190,9 +448,6 @@ reverse_sync() {
 
     log "INFO" "Reverse sync PR created on monorepo"
     echo "pr-created"
-  else
-    log "ERROR" "Josh rejected push — check josh-proxy logs"
-    echo "josh-rejected"
   fi
 }
 
@@ -220,12 +475,7 @@ initial_import() {
   log "INFO" "=== Initial import: subrepo/${subrepo_branch} → mono/${mono_branch}:${subfolder}/ ==="
 
   # 1. Clone monorepo (directly, not through josh — we need the real repo)
-  local mono_auth_url
-  local api_host_path
-  api_host_path=$(echo "$MONOREPO_API" | sed 's|https://||; s|/api/v1/repos/|/|')
-  mono_auth_url="https://${BOT_USER}:${GITEA_TOKEN}@${api_host_path}.git"
-
-  git clone "$mono_auth_url" \
+  git clone "$(mono_auth_url)" \
     --branch "$mono_branch" --single-branch \
     "${work_dir}/monorepo" || die "Failed to clone monorepo"
 
@@ -250,7 +500,7 @@ initial_import() {
 
   mkdir -p "$subfolder"
   rsync -a --exclude='.git' "${work_dir}/subrepo/" "${subfolder}/"
-  git add "$subfolder"
+  git add -f -- "$subfolder"
 
   if git diff --cached --quiet; then
     log "INFO" "No changes — subfolder already matches subrepo"
@@ -268,7 +518,14 @@ ${BOT_TRAILER}: import/${JOSH_SYNC_TARGET_NAME}/${ts}" >&2
 
   # 5. Create PR on monorepo
   local pr_body
-  pr_body="## Initial import\n\nImporting existing subrepo \`${subrepo_branch}\` (${file_count} files) into \`${subfolder}/\`.\n\n**Review checklist:**\n- [ ] Content looks correct\n- [ ] No leaked credentials or environment-specific config\n- [ ] CI passes"
+  pr_body="## Initial import
+
+Importing existing subrepo \`${subrepo_branch}\` (${file_count} files) into \`${subfolder}/\`.
+
+**Review checklist:**
+- [ ] Content looks correct
+- [ ] No leaked credentials or environment-specific config
+- [ ] CI passes"
 
   create_pr "${MONOREPO_API}" "${GITEA_TOKEN}" \
     "$mono_branch" "$staging_branch" \

schema/config-schema.json

@@ -3,11 +3,16 @@
   "title": "josh-sync configuration",
   "description": "Configuration for bidirectional monorepo ↔ subrepo sync via josh-proxy",
   "type": "object",
-  "required": ["josh", "targets", "bot"],
+  "required": ["schema_version", "josh", "targets", "bot"],
   "properties": {
+    "schema_version": {
+      "type": "integer",
+      "const": 2,
+      "description": "Schema version. Required. Must be 2 for josh-sync v2.x configs."
+    },
     "josh": {
       "type": "object",
-      "required": ["proxy_url", "monorepo_path"],
+      "required": ["proxy_url", "monorepo_path", "monorepo_url"],
       "properties": {
         "proxy_url": {
           "type": "string",
@@ -16,7 +21,17 @@
         },
         "monorepo_path": {
           "type": "string",
-          "description": "Repo path as josh sees it (org/repo)"
+          "description": "Repo path as josh-proxy sees it (org/repo)"
+        },
+        "monorepo_url": {
+          "type": "string",
+          "description": "Monorepo git clone URL — git@host:org/repo.git (SSH) or https://host/org/repo.git. The gitea host is derived from this URL."
+        },
+        "monorepo_auth": {
+          "type": "string",
+          "enum": ["https", "ssh"],
+          "default": "https",
+          "description": "Auth method for cloning the monorepo. SSH uses the user's ssh-agent / ~/.ssh/config; HTTPS injects ${SYNC_BOT_USER}:${SYNC_BOT_TOKEN} into the URL."
         }
       }
     },
@@ -70,6 +85,17 @@
             "items": { "type": "string" },
             "default": [],
             "description": "Branches that only sync mono → subrepo (never reverse)"
+          },
+          "exclude": {
+            "type": "array",
+            "items": { "type": "string" },
+            "default": [],
+            "description": "File/directory patterns to exclude from sync via josh :exclude filter. Josh pattern syntax: 'dir/' for directories, '*.ext' for globs, '**/dir/' for nested matches. Patterns are embedded inline in the josh-proxy URL."
+          },
+          "history_lock": {
+            "type": "string",
+            "enum": ["rewrite", "preserve"],
+            "description": "Onboarding strategy override. 'preserve' selects the non-destructive adopt strategy (keeps subrepo history via an adoption merge); 'rewrite' selects the destructive reset strategy (force-pushes josh-filtered history). When omitted, `josh-sync onboard` auto-detects: subrepos with branches → adopt, empty subrepos → reset. The CLI flag `--mode={reset,adopt}` overrides this."
           }
         }
       }

tests/fixtures/minimal.yml

@@ -1,7 +1,9 @@
 # Test fixture: minimal single-target config
+schema_version: 2
 josh:
   proxy_url: "https://josh.test.local"
   monorepo_path: "org/repo"
+  monorepo_url: "git@gitea.test.local:org/repo.git"
 
 targets:
   - name: "example"

tests/fixtures/multi-target.yml

@@ -1,7 +1,9 @@
 # Test fixture: multi-target config
+schema_version: 2
 josh:
   proxy_url: "https://josh.test.local"
   monorepo_path: "org/monorepo"
+  monorepo_url: "git@gitea.test.local:org/monorepo.git"
 
 targets:
   - name: "app-a"

tests/unit/action.bats

@@ -0,0 +1,17 @@
+#!/usr/bin/env bats
+# tests/unit/action.bats — Composite action regression tests
+
+setup() {
+  JOSH_SYNC_ROOT="$(cd "$BATS_TEST_DIRNAME/../.." && pwd)"
+  ACTION_FILE="${JOSH_SYNC_ROOT}/action.yml"
+}
+
+@test "forward sync is not globally skipped when HEAD has the sync trailer" {
+  ! grep -q "Loop guard (forward)" "$ACTION_FILE"
+  ! grep -q "HEAD commit has sync trailer" "$ACTION_FILE"
+  ! grep -q "steps.guard.outputs.skip" "$ACTION_FILE"
+}
+
+@test "composite action still invokes the josh-sync CLI" {
+  grep -q "josh-sync sync" "$ACTION_FILE"
+}

tests/unit/adopt.bats

@@ -0,0 +1,92 @@
+#!/usr/bin/env bats
+# tests/unit/adopt.bats — Non-destructive adoption merge tests
+
+setup() {
+  export JOSH_SYNC_ROOT="$(cd "$BATS_TEST_DIRNAME/../.." && pwd)"
+  source "$JOSH_SYNC_ROOT/lib/core.sh"
+  source "$JOSH_SYNC_ROOT/lib/adopt.sh"
+
+  TEST_ROOT="$(mktemp -d)"
+  export BOT_NAME="test-bot"
+  export BOT_EMAIL="test-bot@test.local"
+  export BOT_TRAILER="Josh-Sync-Origin"
+  export JOSH_SYNC_TARGET_NAME="example"
+  export SYNC_BRANCH_MONO="main"
+  export SYNC_BRANCH_SUBREPO="main"
+}
+
+teardown() {
+  rm -rf "$TEST_ROOT"
+}
+
+make_bare_repo() {
+  local name="$1"
+  local content="$2"
+  local message="$3"
+  local work="${TEST_ROOT}/${name}-work"
+  local bare="${TEST_ROOT}/${name}.git"
+
+  git init "$work" >/dev/null
+  git -C "$work" checkout -b main >/dev/null
+  git -C "$work" config user.name "Test User"
+  git -C "$work" config user.email "test@test.local"
+  printf '%s\n' "$content" > "${work}/README.md"
+  git -C "$work" add README.md
+  git -C "$work" commit -m "$message" >/dev/null
+
+  git init --bare "$bare" >/dev/null
+  git -C "$work" remote add origin "$bare"
+  git -C "$work" push origin main >/dev/null
+  printf '%s\n' "$bare"
+}
+
+subrepo_auth_url() {
+  printf '%s\n' "$SUBREPO_BARE"
+}
+
+josh_auth_url() {
+  printf '%s\n' "$JOSH_BARE"
+}
+
+@test "adopt_branch creates merge with josh head first parent and subrepo head second parent" {
+  SUBREPO_BARE="$(make_bare_repo subrepo "same tree" "subrepo history")"
+  JOSH_BARE="$(make_bare_repo josh "same tree" "josh filtered history")"
+
+  local old_subrepo_head josh_head josh_tree result adopt_head
+  old_subrepo_head=$(git --git-dir="$SUBREPO_BARE" rev-parse main)
+  josh_head=$(git --git-dir="$JOSH_BARE" rev-parse main)
+  josh_tree=$(git --git-dir="$JOSH_BARE" rev-parse 'main^{tree}')
+
+  result=$(adopt_branch)
+
+  [ "$result" = "adopted" ]
+  adopt_head=$(git --git-dir="$SUBREPO_BARE" rev-parse main)
+  [ "$adopt_head" != "$old_subrepo_head" ]
+  [ "$(git --git-dir="$SUBREPO_BARE" rev-parse 'main^1')" = "$josh_head" ]
+  [ "$(git --git-dir="$SUBREPO_BARE" rev-parse 'main^2')" = "$old_subrepo_head" ]
+  [ "$(git --git-dir="$SUBREPO_BARE" rev-parse 'main^{tree}')" = "$josh_tree" ]
+}
+
+@test "adopt_branch aborts when trees differ and leaves subrepo head unchanged" {
+  SUBREPO_BARE="$(make_bare_repo subrepo "subrepo tree" "subrepo history")"
+  JOSH_BARE="$(make_bare_repo josh "josh tree" "josh filtered history")"
+
+  local old_subrepo_head result
+  old_subrepo_head=$(git --git-dir="$SUBREPO_BARE" rev-parse main)
+
+  result=$(adopt_branch)
+
+  [ "$result" = "tree-mismatch" ]
+  [ "$(git --git-dir="$SUBREPO_BARE" rev-parse main)" = "$old_subrepo_head" ]
+}
+
+@test "adopt_branch reports missing subrepo branch before cloning" {
+  SUBREPO_BARE="$(make_bare_repo subrepo "same tree" "subrepo history")"
+  JOSH_BARE="$(make_bare_repo josh "same tree" "josh filtered history")"
+  export SYNC_BRANCH_SUBREPO="missing"
+
+  local result
+  result=$(adopt_branch)
+
+  [ "$result" = "missing-branch" ]
+}

tests/unit/adopt_e2e.bats

@@ -0,0 +1,697 @@
+#!/usr/bin/env bats
+
+bats_require_minimum_version 1.5.0
+
+# tests/unit/adopt_e2e.bats — End-to-end adopt behaviour and ADR cross-cuts
+#
+# Covers the goal-1 scenarios from the adopt unification plan:
+#   - tree-equality rejection (clear hint + no commit on subrepo)
+#   - already-adopted idempotency
+#   - merge commit shape (ADR-005 trailer, ADR-008 first-parent walk)
+#   - fast-forward push semantics (success + push-rejected surfacing)
+#   - reverse-sync loop guard (ADR-005)
+#   - linearize-fallback selection invariant (ADR-011)
+#   - checkpoint/resume at each adopt_flow step (ADR-010)
+#
+# Tests run against real local bare repos — no mocking of the git layer.
+
+setup() {
+  export JOSH_SYNC_ROOT="$(cd "$BATS_TEST_DIRNAME/../.." && pwd)"
+  source "$JOSH_SYNC_ROOT/lib/core.sh"
+  source "$JOSH_SYNC_ROOT/lib/state.sh"
+  source "$JOSH_SYNC_ROOT/lib/auth.sh"
+  source "$JOSH_SYNC_ROOT/lib/adopt.sh"
+  source "$JOSH_SYNC_ROOT/lib/onboard.sh"
+
+  TEST_ROOT="$(mktemp -d)"
+  export BOT_NAME="test-bot"
+  export BOT_EMAIL="test-bot@test.local"
+  export BOT_TRAILER="Josh-Sync-Origin"
+  export JOSH_SYNC_TARGET_NAME="example"
+  export SYNC_BRANCH_MONO="main"
+  export SYNC_BRANCH_SUBREPO="main"
+
+  # Test-local auth shims must be defined AFTER sourcing lib/auth.sh, otherwise
+  # the lib's real subrepo_auth_url / josh_auth_url (which need SUBREPO_URL,
+  # BOT_USER, etc.) overrides our bare-repo shortcut.
+  subrepo_auth_url() { printf '%s\n' "${SUBREPO_BARE:-}"; }
+  josh_auth_url()    { printf '%s\n' "${JOSH_BARE:-}"; }
+}
+
+teardown() {
+  # Restore cwd before the rm — setup_state_monorepo cd's into a dir that's
+  # about to be deleted, and bats doesn't reset cwd between tests.
+  cd "$BATS_TEST_DIRNAME" 2>/dev/null || true
+  rm -rf "$TEST_ROOT"
+}
+
+# ─── Helpers ────────────────────────────────────────────────────────
+
+# Build a fresh bare repo seeded with one commit; returns the bare path on stdout.
+make_bare_repo() {
+  local name="$1"
+  local content="$2"
+  local message="$3"
+  local work="${TEST_ROOT}/${name}-work"
+  local bare="${TEST_ROOT}/${name}.git"
+
+  git init "$work" >/dev/null
+  git -C "$work" checkout -b main >/dev/null
+  git -C "$work" config user.name "Test User"
+  git -C "$work" config user.email "test@test.local"
+  printf '%s\n' "$content" > "${work}/README.md"
+  git -C "$work" add README.md
+  git -C "$work" commit -m "$message" >/dev/null
+
+  git init --bare "$bare" >/dev/null
+  # Make HEAD on the bare point at main so later clones don't land on master.
+  git -C "$bare" symbolic-ref HEAD refs/heads/main
+  git -C "$work" remote add origin "$bare"
+  git -C "$work" push origin main >/dev/null
+  printf '%s\n' "$bare"
+}
+
+# Append a commit to an existing bare repo. If $3 is empty, makes an empty commit
+# (tree unchanged) so first-parent walks have something to observe.
+add_commit_to_bare() {
+  local bare="$1"
+  local message="$2"
+  local content="${3:-}"
+  local work="${TEST_ROOT}/add-${RANDOM}-$$"
+  git clone "$bare" "$work" >/dev/null 2>&1
+  git -C "$work" config user.name "Test User"
+  git -C "$work" config user.email "test@test.local"
+  if [ -n "$content" ]; then
+    printf '%s\n' "$content" >> "${work}/README.md"
+    git -C "$work" commit -am "$message" >/dev/null
+  else
+    git -C "$work" commit --allow-empty -m "$message" >/dev/null
+  fi
+  git -C "$work" push origin main >/dev/null 2>&1
+}
+
+# Stand up a local working "monorepo" with an `origin` bare remote and cd into
+# it. Gives lib/state.sh helpers (worktree + push to origin) something real to
+# work against.
+setup_state_monorepo() {
+  local mono_work="${TEST_ROOT}/mono"
+  local mono_bare="${TEST_ROOT}/mono.git"
+  git init -q "$mono_work"
+  git -C "$mono_work" checkout -q -b main
+  git -C "$mono_work" config user.name "Test User"
+  git -C "$mono_work" config user.email "test@test.local"
+  printf 'mono\n' > "${mono_work}/README.md"
+  git -C "$mono_work" add README.md
+  git -C "$mono_work" commit -q -m "initial"
+  git init -q --bare "$mono_bare"
+  git -C "$mono_work" remote add origin "$mono_bare"
+  git -C "$mono_work" push -q origin main
+  cd "$mono_work"
+}
+
+# adopt_branch is defined as a subshell function (`adopt_branch() ( ... )`) in
+# lib/adopt.sh so its EXIT trap stays contained — no helper needed here.
+adopt_branch_quietly() {
+  adopt_branch >/dev/null
+}
+
+# ─── Tree-mismatch surfacing ────────────────────────────────────────
+
+@test "adopt_branch tree-mismatch error message points the user at the import PR" {
+  SUBREPO_BARE="$(make_bare_repo subrepo "subrepo content" "subrepo history")"
+  JOSH_BARE="$(make_bare_repo josh "josh content" "josh filtered history")"
+
+  local combined
+  combined=$(adopt_branch 2>&1)
+
+  [[ "$combined" == *"merge the import PR"* ]]
+}
+
+@test "adopt_branch tree-mismatch creates no commit on the subrepo (clean abort)" {
+  SUBREPO_BARE="$(make_bare_repo subrepo "subrepo content" "subrepo history")"
+  JOSH_BARE="$(make_bare_repo josh "josh content" "josh filtered history")"
+
+  local before_count before_head after_count after_head
+  before_count=$(git --git-dir="$SUBREPO_BARE" rev-list --count main)
+  before_head=$(git --git-dir="$SUBREPO_BARE" rev-parse main)
+
+  adopt_branch_quietly 2>&1
+
+  after_count=$(git --git-dir="$SUBREPO_BARE" rev-list --count main)
+  after_head=$(git --git-dir="$SUBREPO_BARE" rev-parse main)
+  [ "$before_count" = "$after_count" ]
+  [ "$before_head" = "$after_head" ]
+}
+
+# ─── Idempotency ────────────────────────────────────────────────────
+
+@test "adopt_branch is idempotent — second invocation returns already-adopted, no new commit" {
+  SUBREPO_BARE="$(make_bare_repo subrepo "same tree" "subrepo history")"
+  JOSH_BARE="$(make_bare_repo josh "same tree" "josh filtered history")"
+
+  local first_result first_head first_count
+  first_result=$(adopt_branch)
+  first_head=$(git --git-dir="$SUBREPO_BARE" rev-parse main)
+  first_count=$(git --git-dir="$SUBREPO_BARE" rev-list --count main)
+
+  local second_result second_head second_count
+  second_result=$(adopt_branch)
+  second_head=$(git --git-dir="$SUBREPO_BARE" rev-parse main)
+  second_count=$(git --git-dir="$SUBREPO_BARE" rev-list --count main)
+
+  [ "$first_result" = "adopted" ]
+  [ "$second_result" = "already-adopted" ]
+  [ "$first_head" = "$second_head" ]
+  [ "$first_count" = "$second_count" ]
+}
+
+# ─── Merge commit shape ─────────────────────────────────────────────
+
+@test "adopt_branch merge carries the configured bot trailer (ADR-005)" {
+  SUBREPO_BARE="$(make_bare_repo subrepo "same tree" "subrepo history")"
+  JOSH_BARE="$(make_bare_repo josh "same tree" "josh filtered history")"
+
+  adopt_branch_quietly
+
+  local merge_msg
+  merge_msg=$(git --git-dir="$SUBREPO_BARE" log -1 --format=%B main)
+  [[ "$merge_msg" == *"${BOT_TRAILER}: adopt/${SYNC_BRANCH_MONO}/"* ]]
+}
+
+@test "adopt_branch merge places josh-filtered HEAD as parent 1 — first-parent walk reaches monorepo (ADR-008)" {
+  SUBREPO_BARE="$(make_bare_repo subrepo "same tree" "subrepo c1")"
+  add_commit_to_bare "$SUBREPO_BARE" "subrepo c2"
+
+  JOSH_BARE="$(make_bare_repo josh "same tree" "josh c1")"
+  add_commit_to_bare "$JOSH_BARE" "josh c2"
+
+  adopt_branch_quietly
+
+  # First-parent walk from the adoption merge follows the josh chain (parent 1)
+  # and never visits subrepo-only history. If parent ordering ever flipped, the
+  # subrepo commits would appear here — which is exactly the failure mode that
+  # corrupted the monorepo branch in ADR-008.
+  local first_parent_msgs
+  first_parent_msgs=$(git --git-dir="$SUBREPO_BARE" log --first-parent --format=%s main)
+  [[ "$first_parent_msgs" == *"josh c1"* ]]
+  [[ "$first_parent_msgs" == *"josh c2"* ]]
+  [[ "$first_parent_msgs" != *"subrepo c1"* ]]
+  [[ "$first_parent_msgs" != *"subrepo c2"* ]]
+}
+
+# ─── Fast-forward push semantics ────────────────────────────────────
+
+@test "adopt_branch fast-forwards without --force, leaving old subrepo HEAD reachable" {
+  SUBREPO_BARE="$(make_bare_repo subrepo "same tree" "subrepo history")"
+  JOSH_BARE="$(make_bare_repo josh "same tree" "josh filtered history")"
+
+  local old_head result new_head
+  old_head=$(git --git-dir="$SUBREPO_BARE" rev-parse main)
+  result=$(adopt_branch)
+  new_head=$(git --git-dir="$SUBREPO_BARE" rev-parse main)
+
+  [ "$result" = "adopted" ]
+  [ "$new_head" != "$old_head" ]
+  # The original subrepo HEAD must still be an ancestor of the new HEAD —
+  # nothing was rewritten. This is what makes the push a real fast-forward.
+  git --git-dir="$SUBREPO_BARE" merge-base --is-ancestor "$old_head" "$new_head"
+}
+
+@test "adopt_branch surfaces push-rejected when the bare subrepo rejects the push (simulated 'subrepo moved')" {
+  SUBREPO_BARE="$(make_bare_repo subrepo "same tree" "subrepo history")"
+  JOSH_BARE="$(make_bare_repo josh "same tree" "josh filtered history")"
+
+  # Equivalent observable behaviour to "subrepo HEAD changed mid-flight": the
+  # fast-forward push fails. Install a pre-receive hook that rejects
+  # deterministically — adopt_branch's else-branch should surface push-rejected.
+  printf '%s\n' \
+    '#!/usr/bin/env bash' \
+    'echo "subrepo changed during adoption" >&2' \
+    'exit 1' \
+    > "${SUBREPO_BARE}/hooks/pre-receive"
+  chmod +x "${SUBREPO_BARE}/hooks/pre-receive"
+
+  local before_head result after_head
+  before_head=$(git --git-dir="$SUBREPO_BARE" rev-parse main)
+  result=$(adopt_branch 2>/dev/null)
+  after_head=$(git --git-dir="$SUBREPO_BARE" rev-parse main)
+
+  [ "$result" = "push-rejected" ]
+  [ "$before_head" = "$after_head" ]
+}
+
+# ─── Reverse-sync loop guard (ADR-005) ──────────────────────────────
+
+@test "adoption merge is invisible to reverse-sync bot-trailer filter (no re-ingestion loop)" {
+  SUBREPO_BARE="$(make_bare_repo subrepo "same tree" "subrepo history")"
+  JOSH_BARE="$(make_bare_repo josh "same tree" "josh filtered history")"
+
+  local josh_head
+  josh_head=$(git --git-dir="$JOSH_BARE" rev-parse main)
+
+  adopt_branch_quietly
+
+  # Mirror reverse_sync's exact query (lib/sync.sh):
+  #   base = merge-base(mono-filtered/<branch>, HEAD)
+  #   human_commits = git log --ancestry-path "$base..HEAD" \
+  #                   --invert-grep --grep="^${BOT_TRAILER}:"
+  # --ancestry-path is critical: without it, the subrepo's parent-2 orphan
+  # commit (no trailer, real user commit) would show up as a "human commit"
+  # and reverse sync would try to re-ingest the adoption merge's other side.
+  local merge_sha base human_commits
+  merge_sha=$(git --git-dir="$SUBREPO_BARE" rev-parse main)
+  base=$(git --git-dir="$SUBREPO_BARE" merge-base "$josh_head" "$merge_sha")
+  human_commits=$(git --git-dir="$SUBREPO_BARE" log \
+    --ancestry-path "${base}..${merge_sha}" \
+    --invert-grep --grep="^${BOT_TRAILER}:" \
+    --oneline)
+
+  [ -z "$human_commits" ]
+}
+
+# ─── Linearize fallback (ADR-011) ───────────────────────────────────
+
+@test "linearize-fallback commit selection excludes the adopt merge but keeps human commits on top" {
+  SUBREPO_BARE="$(make_bare_repo subrepo "same tree" "subrepo history")"
+  JOSH_BARE="$(make_bare_repo josh "same tree" "josh filtered history")"
+
+  local josh_head
+  josh_head=$(git --git-dir="$JOSH_BARE" rev-parse main)
+
+  adopt_branch_quietly
+
+  # Real human commit on top of the adoption merge.
+  add_commit_to_bare "$SUBREPO_BARE" "human: add note" "human change"
+
+  # Replicate reverse_sync's linearize walk exactly (lib/sync.sh):
+  #   base = merge-base(mono-filtered/<branch>, HEAD)
+  #   commits = git log --ancestry-path "$base..HEAD" --reverse \
+  #             --format=%H --invert-grep --grep="^${BOT_TRAILER}:"
+  # With messy upstream (adopt-merge in the path), linearize must skip the
+  # merge (trailer-filtered) and cherry-pick only the human commit.
+  local work base picked
+  work="${TEST_ROOT}/linearize-walk"
+  git clone "$SUBREPO_BARE" "$work" >/dev/null 2>&1
+  base=$(git -C "$work" merge-base "$josh_head" HEAD)
+  picked=$(git -C "$work" log --ancestry-path "${base}..HEAD" \
+    --reverse --format=%s --invert-grep --grep="^${BOT_TRAILER}:")
+
+  [[ "$picked" == *"human: add note"* ]]
+  [[ "$picked" != *"Adopt ${JOSH_SYNC_TARGET_NAME} for josh-sync"* ]]
+}
+
+# ─── Checkpoint / resume (ADR-010) — strategy=adopt path through onboard_flow
+
+# Stubs that run inside $(...) subshells can't increment shell variables in
+# the parent. Track invocations via append-only files instead and count bytes.
+call_log() { printf '.' >> "${TEST_ROOT}/${1}.log"; }
+call_count() {
+  local f="${TEST_ROOT}/${1}.log"
+  if [ -f "$f" ]; then wc -c < "$f" | tr -d ' '; else echo 0; fi
+}
+
+@test "write_onboard_state then read_onboard_state round-trips the JSON" {
+  setup_state_monorepo
+
+  write_onboard_state "$JOSH_SYNC_TARGET_NAME" \
+    '{"step":"adopting","strategy":"adopt","import_prs":{"main":42},"adopted_branches":[]}'
+
+  local got
+  got=$(read_onboard_state "$JOSH_SYNC_TARGET_NAME")
+  [ "$(echo "$got" | jq -r '.step')" = "adopting" ]
+  [ "$(echo "$got" | jq -r '.strategy')" = "adopt" ]
+  [ "$(echo "$got" | jq -r '.import_prs.main')" = "42" ]
+}
+
+@test "read_onboard_state falls back to legacy <target>/adopt.json with implicit strategy=adopt" {
+  setup_state_monorepo
+
+  # Simulate a state branch where only the v2.1-era adopt.json exists (e.g.,
+  # an adoption started before the unification). Write directly to the state
+  # branch under the legacy filename, without the new strategy field.
+  local tmp
+  tmp=$(mktemp -d)
+  git worktree add --detach "$tmp" >/dev/null 2>&1
+  ( cd "$tmp" && git checkout -q --orphan "$STATE_BRANCH" && { git rm -rfq . 2>/dev/null || true; }
+    mkdir -p "$JOSH_SYNC_TARGET_NAME"
+    printf '%s\n' '{"step":"adopting","import_prs":{},"adopted_branches":[]}' \
+      > "${JOSH_SYNC_TARGET_NAME}/adopt.json"
+    git add -A
+    git -c user.name="$BOT_NAME" -c user.email="$BOT_EMAIL" \
+      commit -q -m "legacy adopt state"
+    git push -q origin "HEAD:${STATE_BRANCH}" )
+  git worktree remove "$tmp" 2>/dev/null || rm -rf "$tmp"
+
+  local got
+  got=$(read_onboard_state "$JOSH_SYNC_TARGET_NAME")
+  [ "$(echo "$got" | jq -r '.step')" = "adopting" ]
+  [ "$(echo "$got" | jq -r '.strategy')" = "adopt" ]
+}
+
+@test "onboard_flow resumes from step=importing (strategy=adopt) — runs import, falls through wait, finalizes via adopt_branch" {
+  setup_state_monorepo
+  write_onboard_state "$JOSH_SYNC_TARGET_NAME" \
+    '{"step":"importing","strategy":"adopt","import_prs":{},"adopted_branches":[]}'
+
+  initial_import() { call_log import; echo "skip"; }
+  adopt_branch()   { call_log adopt;  echo "adopted"; }
+  subrepo_reset()  { call_log reset;  echo "reset"; }
+  get_pr()         { echo '{"merged":true}'; }
+  list_open_prs()  { echo '[]'; }
+
+  local target_json='{"name":"example","branches":{"main":"main"}}'
+  onboard_flow "$target_json" "false" "" >/dev/null 2>&1
+
+  [ "$(call_count import)" = "1" ]
+  [ "$(call_count adopt)" = "1" ]
+  [ "$(call_count reset)" = "0" ]
+  local final
+  final=$(read_onboard_state "$JOSH_SYNC_TARGET_NAME")
+  [ "$(echo "$final" | jq -r '.step')" = "complete" ]
+  [ "$(echo "$final" | jq -r '.strategy')" = "adopt" ]
+}
+
+@test "onboard_flow resumes from step=waiting-for-merge (strategy=adopt) — confirms merged PR, finalizes via adopt_branch" {
+  setup_state_monorepo
+  write_onboard_state "$JOSH_SYNC_TARGET_NAME" \
+    '{"step":"waiting-for-merge","strategy":"adopt","import_prs":{"main":42},"adopted_branches":[]}'
+
+  initial_import() { call_log import; echo "skip"; }
+  adopt_branch()   { call_log adopt;  echo "adopted"; }
+  subrepo_reset()  { call_log reset;  echo "reset"; }
+  get_pr()         { echo '{"merged":true}'; }
+  list_open_prs()  { echo '[]'; }
+  export MONOREPO_API="http://stub" GITEA_TOKEN="stub"
+
+  local target_json='{"name":"example","branches":{"main":"main"}}'
+  onboard_flow "$target_json" "false" "" <<< "" >/dev/null 2>&1
+
+  [ "$(call_count import)" = "0" ]
+  [ "$(call_count adopt)" = "1" ]
+  [ "$(call_count reset)" = "0" ]
+  local final
+  final=$(read_onboard_state "$JOSH_SYNC_TARGET_NAME")
+  [ "$(echo "$final" | jq -r '.step')" = "complete" ]
+}
+
+@test "onboard_flow resumes from step=adopting (strategy=adopt) — skips importing and waiting-for-merge entirely" {
+  setup_state_monorepo
+  write_onboard_state "$JOSH_SYNC_TARGET_NAME" \
+    '{"step":"adopting","strategy":"adopt","import_prs":{},"adopted_branches":[]}'
+
+  initial_import() { call_log import; echo "skip"; }
+  adopt_branch()   { call_log adopt;  echo "adopted"; }
+  subrepo_reset()  { call_log reset;  echo "reset"; }
+  get_pr()         { echo '{"merged":true}'; }
+  list_open_prs()  { echo '[]'; }
+
+  local target_json='{"name":"example","branches":{"main":"main"}}'
+  onboard_flow "$target_json" "false" "" >/dev/null 2>&1
+
+  [ "$(call_count import)" = "0" ]
+  [ "$(call_count adopt)" = "1" ]
+  [ "$(call_count reset)" = "0" ]
+  local final
+  final=$(read_onboard_state "$JOSH_SYNC_TARGET_NAME")
+  [ "$(echo "$final" | jq -r '.step')" = "complete" ]
+}
+
+@test "onboard_flow with step=complete is a no-op (no import, no finalize)" {
+  setup_state_monorepo
+  write_onboard_state "$JOSH_SYNC_TARGET_NAME" \
+    '{"step":"complete","strategy":"adopt","import_prs":{},"adopted_branches":["main"]}'
+
+  initial_import() { call_log import; echo "skip"; }
+  adopt_branch()   { call_log adopt;  echo "adopted"; }
+  subrepo_reset()  { call_log reset;  echo "reset"; }
+
+  local target_json='{"name":"example","branches":{"main":"main"}}'
+  onboard_flow "$target_json" "false" "" >/dev/null 2>&1
+
+  [ "$(call_count import)" = "0" ]
+  [ "$(call_count adopt)" = "0" ]
+  [ "$(call_count reset)" = "0" ]
+}
+
+@test "onboard_flow --restart with explicit strategy=adopt wipes state and re-runs the full sequence" {
+  setup_state_monorepo
+  write_onboard_state "$JOSH_SYNC_TARGET_NAME" \
+    '{"step":"complete","strategy":"adopt","import_prs":{"main":7},"adopted_branches":["main"]}'
+
+  initial_import() { call_log import; echo "skip"; }
+  adopt_branch()   { call_log adopt;  echo "adopted"; }
+  subrepo_reset()  { call_log reset;  echo "reset"; }
+  get_pr()         { echo '{"merged":true}'; }
+  list_open_prs()  { echo '[]'; }
+
+  local target_json='{"name":"example","branches":{"main":"main"}}'
+  onboard_flow "$target_json" "true" "adopt" >/dev/null 2>&1
+
+  [ "$(call_count import)" = "1" ]
+  [ "$(call_count adopt)" = "1" ]
+  [ "$(call_count reset)" = "0" ]
+}
+
+# ─── Goal 2: strategy resolution precedence ─────────────────────────
+
+@test "resolve_onboard_strategy honours explicit --mode flag above config and auto-detect" {
+  # Config says preserve (would map to adopt); flag should win.
+  local target_json='{"name":"x","history_lock":"preserve"}'
+  local picked
+  picked=$(resolve_onboard_strategy "$target_json" "reset")
+  [ "$picked" = "reset" ]
+}
+
+@test "resolve_onboard_strategy maps history_lock=preserve to adopt" {
+  local target_json='{"name":"x","history_lock":"preserve"}'
+  local picked
+  picked=$(resolve_onboard_strategy "$target_json" "")
+  [ "$picked" = "adopt" ]
+}
+
+@test "resolve_onboard_strategy maps history_lock=rewrite to reset" {
+  local target_json='{"name":"x","history_lock":"rewrite"}'
+  local picked
+  picked=$(resolve_onboard_strategy "$target_json" "")
+  [ "$picked" = "reset" ]
+}
+
+@test "resolve_onboard_strategy auto-detects adopt when subrepo has any branches" {
+  SUBREPO_BARE="$(make_bare_repo subrepo "any" "any")"
+  local target_json='{"name":"x"}'
+  local picked
+  picked=$(resolve_onboard_strategy "$target_json" "")
+  [ "$picked" = "adopt" ]
+}
+
+@test "resolve_onboard_strategy auto-detects reset when subrepo has no branches (empty repo)" {
+  SUBREPO_BARE="${TEST_ROOT}/empty.git"
+  git init -q --bare "$SUBREPO_BARE"
+  local target_json='{"name":"x"}'
+  local picked
+  picked=$(resolve_onboard_strategy "$target_json" "")
+  [ "$picked" = "reset" ]
+}
+
+@test "resolve_onboard_strategy rejects unknown --mode value" {
+  local target_json='{"name":"x"}'
+  run resolve_onboard_strategy "$target_json" "weird"
+  [ "$status" -ne 0 ]
+  [[ "$output" == *"Invalid --mode"* ]]
+}
+
+@test "resolve_onboard_strategy rejects unknown history_lock value" {
+  local target_json='{"name":"x","history_lock":"freeze"}'
+  run resolve_onboard_strategy "$target_json" ""
+  [ "$status" -ne 0 ]
+  [[ "$output" == *"Invalid history_lock"* ]]
+}
+
+# ─── Goal 2: onboard_flow with strategy=reset (regression-preserving) ──
+
+@test "onboard_flow resumes from step=resetting (strategy=reset) — finalizes via subrepo_reset" {
+  setup_state_monorepo
+  write_onboard_state "$JOSH_SYNC_TARGET_NAME" \
+    '{"step":"resetting","strategy":"reset","import_prs":{},"reset_branches":[]}'
+
+  initial_import() { call_log import; echo "skip"; }
+  adopt_branch()   { call_log adopt;  echo "adopted"; }
+  subrepo_reset()  { call_log reset;  echo "reset"; }
+
+  local target_json='{"name":"example","branches":{"main":"main"}}'
+  onboard_flow "$target_json" "false" "" >/dev/null 2>&1
+
+  [ "$(call_count import)" = "0" ]
+  [ "$(call_count adopt)" = "0" ]
+  [ "$(call_count reset)" = "1" ]
+  local final
+  final=$(read_onboard_state "$JOSH_SYNC_TARGET_NAME")
+  [ "$(echo "$final" | jq -r '.step')" = "complete" ]
+  [ "$(echo "$final" | jq -r '.strategy')" = "reset" ]
+}
+
+@test "onboard_flow finalize step (strategy=adopt) drives the real adopt_branch end-to-end against bare repos" {
+  # No stubbing of adopt_branch: this test exercises the full unified
+  # dispatch by pre-seeding state at step=adopting and letting onboard_flow
+  # call adopt_branch for real against local bare repos via the auth-URL
+  # shims. Closes the spec's end-to-end criterion for `onboard --mode=adopt`.
+  setup_state_monorepo
+  SUBREPO_BARE="$(make_bare_repo subrepo "same tree" "subrepo history")"
+  JOSH_BARE="$(make_bare_repo josh "same tree" "josh filtered history")"
+
+  local old_subrepo_head josh_head
+  old_subrepo_head=$(git --git-dir="$SUBREPO_BARE" rev-parse main)
+  josh_head=$(git --git-dir="$JOSH_BARE" rev-parse main)
+
+  write_onboard_state "$JOSH_SYNC_TARGET_NAME" \
+    '{"step":"adopting","strategy":"adopt","import_prs":{},"adopted_branches":[]}'
+
+  local target_json='{"name":"example","branches":{"main":"main"}}'
+  onboard_flow "$target_json" "false" "" >/dev/null 2>&1
+
+  # 1. Subrepo HEAD advanced to a real adoption merge.
+  local new_subrepo_head
+  new_subrepo_head=$(git --git-dir="$SUBREPO_BARE" rev-parse main)
+  [ "$new_subrepo_head" != "$old_subrepo_head" ]
+
+  # 2. Merge shape matches ADR-013: parent 1 = josh_head, parent 2 = old subrepo head.
+  [ "$(git --git-dir="$SUBREPO_BARE" rev-parse 'main^1')" = "$josh_head" ]
+  [ "$(git --git-dir="$SUBREPO_BARE" rev-parse 'main^2')" = "$old_subrepo_head" ]
+
+  # 3. Merge message carries the ADR-005 bot trailer.
+  local merge_msg
+  merge_msg=$(git --git-dir="$SUBREPO_BARE" log -1 --format=%B main)
+  [[ "$merge_msg" == *"${BOT_TRAILER}: adopt/${SYNC_BRANCH_MONO}/"* ]]
+
+  # 4. State advanced to complete and recorded the adopted branch.
+  local final
+  final=$(read_onboard_state "$JOSH_SYNC_TARGET_NAME")
+  [ "$(echo "$final" | jq -r '.step')" = "complete" ]
+  [ "$(echo "$final" | jq -r '.strategy')" = "adopt" ]
+  [ "$(echo "$final" | jq -r '.adopted_branches[0]')" = "main" ]
+}
+
+# ─── Goal 2: legacy adopt.json → onboard.json migration on write ────
+
+@test "after read_onboard_state falls back to legacy adopt.json, the next write lands in onboard.json" {
+  setup_state_monorepo
+
+  # Seed the state branch with ONLY the legacy file (no onboard.json yet).
+  local tmp
+  tmp=$(mktemp -d)
+  git worktree add --detach "$tmp" >/dev/null 2>&1
+  ( cd "$tmp" && git checkout -q --orphan "$STATE_BRANCH" && { git rm -rfq . 2>/dev/null || true; }
+    mkdir -p "$JOSH_SYNC_TARGET_NAME"
+    printf '%s\n' '{"step":"adopting","import_prs":{},"adopted_branches":[]}' \
+      > "${JOSH_SYNC_TARGET_NAME}/adopt.json"
+    git add -A
+    git -c user.name="$BOT_NAME" -c user.email="$BOT_EMAIL" \
+      commit -q -m "legacy adopt state"
+    git push -q origin "HEAD:${STATE_BRANCH}" )
+  git worktree remove "$tmp" 2>/dev/null || rm -rf "$tmp"
+
+  # Read → mutate → write back via the unified helpers.
+  local state
+  state=$(read_onboard_state "$JOSH_SYNC_TARGET_NAME")
+  state=$(echo "$state" | jq '.step = "complete"')
+  write_onboard_state "$JOSH_SYNC_TARGET_NAME" "$state"
+
+  # Fetch a fresh copy of the state branch to see what's actually committed.
+  git fetch origin "$STATE_BRANCH" >/dev/null 2>&1
+
+  # onboard.json now exists with the updated step, strategy preserved.
+  local onboard_json
+  onboard_json=$(git show "origin/${STATE_BRANCH}:${JOSH_SYNC_TARGET_NAME}/onboard.json")
+  [ "$(echo "$onboard_json" | jq -r '.step')" = "complete" ]
+  [ "$(echo "$onboard_json" | jq -r '.strategy')" = "adopt" ]
+
+  # Legacy adopt.json is left in place (harmless; read fallback still resolves).
+  git show "origin/${STATE_BRANCH}:${JOSH_SYNC_TARGET_NAME}/adopt.json" >/dev/null
+}
+
+@test "onboard_flow importing step dies (does not warn-and-continue) when pr_number lookup fails — prevents duplicate import PR on resume" {
+  setup_state_monorepo
+  write_onboard_state "$JOSH_SYNC_TARGET_NAME" \
+    '{"step":"importing","strategy":"adopt","import_prs":{},"adopted_branches":[]}'
+
+  # initial_import claims a PR was created, but list_open_prs returns nothing
+  # matching → pr_number ends up empty. The fix turns the old WARN-and-continue
+  # into a die so a subsequent resume can't re-import and duplicate the PR.
+  initial_import() { echo "pr-created"; }
+  list_open_prs()  { echo '[]'; }
+  adopt_branch()   { echo "adopted"; }
+  export MONOREPO_API="http://stub" GITEA_TOKEN="stub"
+
+  local target_json='{"name":"example","branches":{"main":"main"}}'
+  run --separate-stderr onboard_flow "$target_json" "false" ""
+  [ "$status" -ne 0 ]
+  [[ "$stderr" == *"Could not find import PR number"* ]]
+  [[ "$stderr" == *"duplicate import PR"* ]]
+}
+
+@test "resolve_onboard_strategy dies (does not silently pick reset) when ls-remote against the subrepo fails" {
+  # Point auth at a nonexistent local path so ls-remote fails (exit non-zero).
+  SUBREPO_BARE="${TEST_ROOT}/this-does-not-exist.git"
+  local target_json='{"name":"x"}'
+  run --separate-stderr resolve_onboard_strategy "$target_json" ""
+  [ "$status" -ne 0 ]
+  [[ "$stderr" == *"Cannot auto-detect strategy"* ]]
+}
+
+@test "onboard_flow rejects --mode that conflicts with a strategy already saved in state" {
+  setup_state_monorepo
+  write_onboard_state "$JOSH_SYNC_TARGET_NAME" \
+    '{"step":"adopting","strategy":"adopt","import_prs":{},"adopted_branches":[]}'
+
+  initial_import() { echo "skip"; }
+  adopt_branch()   { echo "adopted"; }
+  subrepo_reset()  { echo "reset"; }
+
+  local target_json='{"name":"example","branches":{"main":"main"}}'
+  run --separate-stderr onboard_flow "$target_json" "false" "reset"
+  [ "$status" -ne 0 ]
+  [[ "$stderr" == *"Saved strategy is 'adopt'"* ]]
+  [[ "$stderr" == *"--restart"* ]]
+}
+
+@test "read_onboard_state injects strategy=reset for legacy v2.1 onboard.json (no .strategy field)" {
+  setup_state_monorepo
+
+  # Seed only a legacy-format onboard.json (no .strategy field).
+  local tmp
+  tmp=$(mktemp -d)
+  git worktree add --detach "$tmp" >/dev/null 2>&1
+  ( cd "$tmp" && git checkout -q --orphan "$STATE_BRANCH" && { git rm -rfq . 2>/dev/null || true; }
+    mkdir -p "$JOSH_SYNC_TARGET_NAME"
+    printf '%s\n' '{"step":"resetting","import_prs":{"main":42},"reset_branches":["main"]}' \
+      > "${JOSH_SYNC_TARGET_NAME}/onboard.json"
+    git add -A
+    git -c user.name="$BOT_NAME" -c user.email="$BOT_EMAIL" \
+      commit -q -m "legacy onboard state"
+    git push -q origin "HEAD:${STATE_BRANCH}" )
+  git worktree remove "$tmp" 2>/dev/null || rm -rf "$tmp"
+
+  local got
+  got=$(read_onboard_state "$JOSH_SYNC_TARGET_NAME")
+  [ "$(echo "$got" | jq -r '.step')" = "resetting" ]
+  [ "$(echo "$got" | jq -r '.strategy')" = "reset" ]
+}
+
+@test "onboard_flow resumes from step=waiting-for-merge (strategy=reset) — transitions to resetting" {
+  setup_state_monorepo
+  write_onboard_state "$JOSH_SYNC_TARGET_NAME" \
+    '{"step":"waiting-for-merge","strategy":"reset","import_prs":{"main":42},"reset_branches":[],"archived_url":"git@host:org/old.git","archived_api":"https://host/api/v1/repos/org/old","archived_auth":"https"}'
+
+  initial_import() { call_log import; echo "skip"; }
+  adopt_branch()   { call_log adopt;  echo "adopted"; }
+  subrepo_reset()  { call_log reset;  echo "reset"; }
+  get_pr()         { echo '{"merged":true}'; }
+  list_open_prs()  { echo '[]'; }
+  export MONOREPO_API="http://stub" GITEA_TOKEN="stub"
+
+  local target_json='{"name":"example","branches":{"main":"main"}}'
+  onboard_flow "$target_json" "false" "" <<< "" >/dev/null 2>&1
+
+  [ "$(call_count adopt)" = "0" ]
+  [ "$(call_count reset)" = "1" ]
+}

tests/unit/auth.bats

@@ -37,3 +37,39 @@ setup() {
   url=$(subrepo_auth_url)
   [ "$url" = "git@gitea.test.local:ext/app-a.git" ]
 }
+
+@test "mono_auth_url returns bare URL for SSH" {
+  export MONOREPO_AUTH="ssh"
+  export MONOREPO_URL="git@code.example.io:org/monorepo.git"
+
+  local url
+  url=$(mono_auth_url)
+  [ "$url" = "git@code.example.io:org/monorepo.git" ]
+}
+
+@test "mono_auth_url injects credentials for HTTPS git@-form monorepo_url" {
+  export MONOREPO_AUTH="https"
+  export MONOREPO_URL="git@code.example.io:org/monorepo.git"
+
+  local url
+  url=$(mono_auth_url)
+  [ "$url" = "https://sync-bot:test-token-123@code.example.io/org/monorepo.git" ]
+}
+
+@test "mono_auth_url injects credentials for HTTPS https-form monorepo_url" {
+  export MONOREPO_AUTH="https"
+  export MONOREPO_URL="https://code.example.io/org/monorepo.git"
+
+  local url
+  url=$(mono_auth_url)
+  [ "$url" = "https://sync-bot:test-token-123@code.example.io/org/monorepo.git" ]
+}
+
+@test "mono_auth_url defaults to HTTPS when MONOREPO_AUTH unset" {
+  unset MONOREPO_AUTH
+  export MONOREPO_URL="https://code.example.io/org/monorepo.git"
+
+  local url
+  url=$(mono_auth_url)
+  [ "$url" = "https://sync-bot:test-token-123@code.example.io/org/monorepo.git" ]
+}

tests/unit/cli.bats

@@ -0,0 +1,123 @@
+#!/usr/bin/env bats
+
+bats_require_minimum_version 1.5.0
+
+# tests/unit/cli.bats — bin/josh-sync CLI surface tests
+#
+# Invokes the CLI as a subprocess (not by sourcing libs) so flag parsing,
+# command dispatch, help/usage text, and the `adopt → onboard --mode=adopt`
+# alias regress cleanly. These tests deliberately stay at the parse/dispatch
+# layer — anything that would reach out to git remotes is set up to fail at
+# target-lookup time, before any side effects.
+#
+# Uses `run --separate-stderr` so we can assert on stderr separately (most of
+# josh-sync's output is logged via core.sh's `log()` which writes to stderr).
+
+setup() {
+  JOSH_SYNC_ROOT="$(cd "$BATS_TEST_DIRNAME/../.." && pwd)"
+  JOSH_BIN="${JOSH_SYNC_ROOT}/bin/josh-sync"
+  FIXTURES="${JOSH_SYNC_ROOT}/tests/fixtures"
+  TEST_ROOT="$(mktemp -d)"
+}
+
+teardown() {
+  cd "$BATS_TEST_DIRNAME" 2>/dev/null || true
+  rm -rf "$TEST_ROOT"
+}
+
+# Drop the minimal fixture config into a clean cwd. Most cmd_* paths read
+# .josh-sync.yml from the working directory.
+seed_minimal_config() {
+  cp "${FIXTURES}/minimal.yml" "${TEST_ROOT}/.josh-sync.yml"
+  cd "$TEST_ROOT"
+}
+
+# ─── Global flags ───────────────────────────────────────────────────
+
+@test "--version exits 0 and prints the version" {
+  run "$JOSH_BIN" --version
+  [ "$status" -eq 0 ]
+  [[ "$output" == *"josh-sync"* ]]
+}
+
+@test "--help exits 0 and advertises onboard, the adopt alias, and --mode" {
+  run "$JOSH_BIN" --help
+  [ "$status" -eq 0 ]
+  # Help text is printed to stderr via `cat >&2`, so combine with --separate.
+  run --separate-stderr "$JOSH_BIN" --help
+  [ "$status" -eq 0 ]
+  [[ "$stderr" == *"onboard <target>"* ]]
+  [[ "$stderr" == *"adopt <target>"* ]]
+  [[ "$stderr" == *"Alias for 'onboard --mode=adopt'"* ]]
+  [[ "$stderr" == *"--mode={reset,adopt}"* ]]
+}
+
+# ─── onboard flag parsing & dispatch ────────────────────────────────
+
+@test "onboard with no target exits non-zero and prints usage including --mode" {
+  seed_minimal_config
+  run --separate-stderr "$JOSH_BIN" onboard
+  [ "$status" -ne 0 ]
+  [[ "$stderr" == *"Usage: josh-sync onboard"* ]]
+  [[ "$stderr" == *"--mode=reset|adopt"* ]]
+}
+
+@test "onboard --mode=invalid is rejected with a clear error" {
+  seed_minimal_config
+  run --separate-stderr "$JOSH_BIN" onboard --mode=invalid example
+  [ "$status" -ne 0 ]
+  [[ "$stderr" == *"Invalid --mode"* ]]
+}
+
+@test "onboard --mode=adopt against an unknown target reports target-not-found" {
+  seed_minimal_config
+  # Proves --mode parses correctly: parse_config succeeds, then cmd_onboard
+  # fails at target lookup, before any git/network activity.
+  run --separate-stderr "$JOSH_BIN" onboard --mode=adopt nonexistent
+  [ "$status" -ne 0 ]
+  [[ "$stderr" == *"not found"* ]]
+}
+
+# ─── adopt alias ────────────────────────────────────────────────────
+
+@test "adopt alias forwards to onboard --mode=adopt (visible via alias log line + target lookup)" {
+  seed_minimal_config
+  run --separate-stderr "$JOSH_BIN" adopt nonexistent
+  [ "$status" -ne 0 ]
+  # Alias notice from cmd_adopt:
+  [[ "$stderr" == *"alias for: josh-sync onboard --mode=adopt"* ]]
+  # And the forwarded call lands in cmd_onboard's target lookup:
+  [[ "$stderr" == *"not found"* ]]
+}
+
+@test "onboard usage listing shows --restart and --mode flags together" {
+  seed_minimal_config
+  run --separate-stderr "$JOSH_BIN" onboard
+  [ "$status" -ne 0 ]
+  [[ "$stderr" == *"--restart"* ]]
+  [[ "$stderr" == *"--mode"* ]]
+}
+
+# ─── --mode value-parsing guards ────────────────────────────────────
+
+@test "onboard --mode (no value) fails with a helpful message instead of crashing on unbound \$2" {
+  seed_minimal_config
+  run --separate-stderr "$JOSH_BIN" onboard example --mode
+  [ "$status" -ne 0 ]
+  [[ "$stderr" == *"--mode requires a value"* ]]
+}
+
+@test "onboard --mode= (empty after equals) is rejected explicitly, not silently ignored" {
+  seed_minimal_config
+  run --separate-stderr "$JOSH_BIN" onboard example --mode=
+  [ "$status" -ne 0 ]
+  [[ "$stderr" == *"Empty --mode="* ]]
+}
+
+@test "adopt alias dies when a conflicting --mode=reset is also passed (instead of silently honouring reset)" {
+  seed_minimal_config
+  run --separate-stderr "$JOSH_BIN" adopt example --mode=reset
+  [ "$status" -ne 0 ]
+  [[ "$stderr" == *"alias for --mode=adopt"* ]]
+  [[ "$stderr" == *"conflicting"* ]]
+}

tests/unit/config.bats

@@ -104,3 +104,151 @@ setup() {
   run bash -c 'source "$JOSH_SYNC_ROOT/lib/core.sh"; source "$JOSH_SYNC_ROOT/lib/config.sh"; parse_config "nonexistent.yml"'
   [ "$status" -ne 0 ]
 }
+
+@test "parse_config fails when schema_version is missing (no v1 fallback)" {
+  cd "$(mktemp -d)"
+  cat > .josh-sync.yml <<'YAML'
+josh:
+  proxy_url: "https://josh.test.local"
+  monorepo_path: "org/repo"
+  monorepo_url: "git@gitea.test.local:org/repo.git"
+targets:
+  - name: "x"
+    subfolder: "x"
+    subrepo_url: "git@gitea.test.local:ext/x.git"
+    branches: { main: main }
+bot:
+  name: "b"
+  email: "b@b"
+  trailer: "T"
+YAML
+  run bash -c 'source "$JOSH_SYNC_ROOT/lib/core.sh"; source "$JOSH_SYNC_ROOT/lib/config.sh"; parse_config ".josh-sync.yml"'
+  [ "$status" -ne 0 ]
+  [[ "$output" == *"schema_version missing"* ]]
+}
+
+@test "parse_config rejects schema_version: 1" {
+  cd "$(mktemp -d)"
+  cat > .josh-sync.yml <<'YAML'
+schema_version: 1
+josh:
+  proxy_url: "https://josh.test.local"
+  monorepo_path: "org/repo"
+  monorepo_url: "git@gitea.test.local:org/repo.git"
+targets:
+  - name: "x"
+    subfolder: "x"
+    subrepo_url: "git@gitea.test.local:ext/x.git"
+    branches: { main: main }
+bot:
+  name: "b"
+  email: "b@b"
+  trailer: "T"
+YAML
+  run bash -c 'source "$JOSH_SYNC_ROOT/lib/core.sh"; source "$JOSH_SYNC_ROOT/lib/config.sh"; parse_config ".josh-sync.yml"'
+  [ "$status" -ne 0 ]
+  [[ "$output" == *"Unsupported schema_version"* ]] || [[ "$output" == *"requires schema_version 2"* ]]
+}
+
+@test "parse_config fails when josh.monorepo_url is missing" {
+  cd "$(mktemp -d)"
+  cat > .josh-sync.yml <<'YAML'
+schema_version: 2
+josh:
+  proxy_url: "https://josh.test.local"
+  monorepo_path: "org/repo"
+targets:
+  - name: "x"
+    subfolder: "x"
+    subrepo_url: "git@gitea.test.local:ext/x.git"
+    branches: { main: main }
+bot:
+  name: "b"
+  email: "b@b"
+  trailer: "T"
+YAML
+  run bash -c 'source "$JOSH_SYNC_ROOT/lib/core.sh"; source "$JOSH_SYNC_ROOT/lib/config.sh"; parse_config ".josh-sync.yml"'
+  [ "$status" -ne 0 ]
+  [[ "$output" == *"monorepo_url"* ]]
+}
+
+@test "parse_config exports MONOREPO_URL, MONOREPO_AUTH, MONOREPO_GITEA_HOST, MONOREPO_REPO_PATH from SSH form" {
+  cd "$(mktemp -d)"
+  cp "$FIXTURES/minimal.yml" .josh-sync.yml
+
+  parse_config ".josh-sync.yml"
+
+  [ "$MONOREPO_URL" = "git@gitea.test.local:org/repo.git" ]
+  [ "$MONOREPO_AUTH" = "https" ]
+  [ "$MONOREPO_GITEA_HOST" = "gitea.test.local" ]
+  [ "$MONOREPO_REPO_PATH" = "org/repo" ]
+}
+
+@test "parse_config derives MONOREPO_GITEA_HOST from HTTPS monorepo_url" {
+  cd "$(mktemp -d)"
+  cat > .josh-sync.yml <<'YAML'
+schema_version: 2
+josh:
+  proxy_url: "https://josh.test.local"
+  monorepo_path: "org/repo"
+  monorepo_url: "https://gitea.example.io/org/repo.git"
+targets:
+  - name: "x"
+    subfolder: "x"
+    subrepo_url: "git@gitea.test.local:ext/x.git"
+    branches: { main: main }
+bot:
+  name: "b"
+  email: "b@b"
+  trailer: "T"
+YAML
+  parse_config ".josh-sync.yml"
+  [ "$MONOREPO_GITEA_HOST" = "gitea.example.io" ]
+  [ "$MONOREPO_REPO_PATH" = "org/repo" ]
+}
+
+@test "parse_config derives MONOREPO_API from monorepo_url's host (cross-host: monorepo and target on different hosts)" {
+  cd "$(mktemp -d)"
+  cat > .josh-sync.yml <<'YAML'
+schema_version: 2
+josh:
+  proxy_url: "https://josh.example.io"
+  monorepo_path: "org/repo"
+  monorepo_url: "git@code.example.io:org/repo.git"
+targets:
+  - name: "x"
+    subfolder: "x"
+    subrepo_url: "git@other-host.io:ext/x.git"
+    branches: { main: main }
+bot:
+  name: "b"
+  email: "b@b"
+  trailer: "T"
+YAML
+  parse_config ".josh-sync.yml"
+  [ "$MONOREPO_API" = "https://code.example.io/api/v1/repos/org/repo" ]
+}
+
+@test "parse_config rejects invalid monorepo_auth value" {
+  cd "$(mktemp -d)"
+  cat > .josh-sync.yml <<'YAML'
+schema_version: 2
+josh:
+  proxy_url: "https://josh.test.local"
+  monorepo_path: "org/repo"
+  monorepo_url: "git@gitea.test.local:org/repo.git"
+  monorepo_auth: "weird"
+targets:
+  - name: "x"
+    subfolder: "x"
+    subrepo_url: "git@gitea.test.local:ext/x.git"
+    branches: { main: main }
+bot:
+  name: "b"
+  email: "b@b"
+  trailer: "T"
+YAML
+  run bash -c 'source "$JOSH_SYNC_ROOT/lib/core.sh"; source "$JOSH_SYNC_ROOT/lib/config.sh"; parse_config ".josh-sync.yml"'
+  [ "$status" -ne 0 ]
+  [[ "$output" == *"monorepo_auth"* ]]
+}

tests/unit/sync.bats

@@ -0,0 +1,90 @@
+#!/usr/bin/env bats
+# tests/unit/sync.bats — Sync/import algorithm tests
+
+setup() {
+  export JOSH_SYNC_ROOT="$(cd "$BATS_TEST_DIRNAME/../.." && pwd)"
+  source "$JOSH_SYNC_ROOT/lib/core.sh"
+  source "$JOSH_SYNC_ROOT/lib/sync.sh"
+
+  TEST_ROOT="$(mktemp -d)"
+  export BOT_NAME="test-bot"
+  export BOT_EMAIL="test-bot@test.local"
+  export BOT_TRAILER="Josh-Sync-Origin"
+  export GITEA_TOKEN="test-token"
+  export MONOREPO_API="https://gitea.test.local/api/v1/repos/org/mono"
+  export JOSH_SYNC_TARGET_NAME="crm"
+  export JOSH_SYNC_TARGETS='[{"name":"crm","subfolder":"apps/crm"}]'
+  export SYNC_BRANCH_MONO="main"
+  export SYNC_BRANCH_SUBREPO="main"
+}
+
+teardown() {
+  rm -rf "$TEST_ROOT"
+}
+
+make_mono_repo() {
+  local work="${TEST_ROOT}/mono-work"
+  local bare="${TEST_ROOT}/mono.git"
+
+  git init "$work" >/dev/null
+  git -C "$work" checkout -b main >/dev/null
+  git -C "$work" config user.name "Test User"
+  git -C "$work" config user.email "test@test.local"
+  printf 'mono\n' > "${work}/README.md"
+  git -C "$work" add README.md
+  git -C "$work" commit -m "mono base" >/dev/null
+
+  git init --bare "$bare" >/dev/null
+  git -C "$work" remote add origin "$bare"
+  git -C "$work" push origin main >/dev/null
+  printf '%s\n' "$bare"
+}
+
+make_subrepo_with_tracked_ignored_file() {
+  local work="${TEST_ROOT}/subrepo-work"
+  local bare="${TEST_ROOT}/subrepo.git"
+
+  git init "$work" >/dev/null
+  git -C "$work" checkout -b main >/dev/null
+  git -C "$work" config user.name "Test User"
+  git -C "$work" config user.email "test@test.local"
+
+  mkdir -p "${work}/.dependencies"
+  printf '.dependencies/\n' > "${work}/.gitignore"
+  printf 'visible\n' > "${work}/visible.txt"
+  printf 'tracked even though ignored\n' > "${work}/.dependencies/tracked.txt"
+
+  git -C "$work" add .gitignore visible.txt
+  git -C "$work" add -f .dependencies/tracked.txt
+  git -C "$work" commit -m "subrepo with tracked ignored file" >/dev/null
+
+  git init --bare "$bare" >/dev/null
+  git -C "$work" remote add origin "$bare"
+  git -C "$work" push origin main >/dev/null
+  printf '%s\n' "$bare"
+}
+
+mono_auth_url() {
+  printf '%s\n' "$MONO_BARE"
+}
+
+subrepo_auth_url() {
+  printf '%s\n' "$SUBREPO_BARE"
+}
+
+create_pr() {
+  printf '%s\n' "$4" > "${TEST_ROOT}/created-pr-head"
+}
+
+@test "initial_import stages files tracked in subrepo even when ignored by copied .gitignore" {
+  MONO_BARE="$(make_mono_repo)"
+  SUBREPO_BARE="$(make_subrepo_with_tracked_ignored_file)"
+
+  local result import_branch
+  result="$(initial_import)"
+  import_branch="$(cat "${TEST_ROOT}/created-pr-head")"
+
+  [ "$result" = "pr-created" ]
+  git --git-dir="$MONO_BARE" ls-tree -r --name-only "$import_branch" \
+    | grep -q '^apps/crm/.dependencies/tracked.txt$'
+}