Fix #2626: orchestrator pre-sync commit no longer deletes agent-pushed files

[jwbron]

Summary

Closes #2626.

_commit_statefiles_to_worktree runs at every phase boundary to capture the orchestrator's live .egg-state/ writes before _sync_worktree_with_remote. In #2626 it instead landed a commit that deleted the plan draft and agent-outputs that BRC consensus had just produced — observed on issue-1557-v2 plan phase (d4a7dc974) and also at the refine boundary (8a6d96bb2), so this is a class issue at every phase, not plan-specific.

Root cause is two compounding bugs:

1. Cross-worktree branch-ref advance. Agents are taught (sandbox/agent-config/rules/branch-recovery.md, plus the gateway's detached-HEAD commit hint) to run git update-ref refs/heads/<assigned-branch> <sha> after a detached commit. update-ref is plumbing and does not honour per-worktree branch locks, so the call from a per-agent worktree silently advances the shared refs/heads/<pipeline-branch> ref the orchestrator's worktree has checked out. The orchestrator's HEAD symref jumps to the agent's commit; its index and working tree stay at the prior state. git status then reports every agent-pushed file under .egg-state/ as a staged deletion.

2. git commit -- <pathspec> auto-stages working-tree changes. The final commit used git commit -m ... -- .egg-state/, which defaults to --only semantics — pulls working-tree changes (including deletions) for the named paths into the commit independent of any explicit git add. In the cross-worktree-advance state, this also committed the working-tree gap (files in HEAD but absent on disk) as real deletes.

The fix:

• _read_tree_head(git_base) just before git add refreshes the index to match HEAD without touching the working tree, so the stale-index-vs-HEAD deletions stop showing up.
• Drop the -- .egg-state/ pathspec from git commit; only what git add --force staged is committed.

Scope

This addresses the delete-commit symptom only. The contract on origin still ends up unpopulated downstream because _populate_contract_from_plan_safe reads the plan draft from the orchestrator's stale working tree, not from HEAD — see the comments on #2626 and the recovery flow there. That gap, plus #2627's "fail if contract is empty" guard, are separate follow-ups.

The mechanism analysis (verified end-to-end with a real git reproduction) is in #2626 (comment).

Test plan

• New test_commit_statefiles_cross_worktree_ref_advance.py — two test cases against the production helper with real git worktree plumbing:
  • Positive: orchestrator's contract write + agent's update-ref recovery, helper runs, asserts plan draft + architect output remain reachable from HEAD post-commit.
  • Idempotent: no orchestrator writes + cross-worktree advance ⇒ helper short-circuits without a commit (previously would have landed a delete-only commit).
• orchestrator/tests/test_commit_statefiles_scoping.py — adjusted test_none_identifier_stages_everything to locate the git add call by subcommand (helper now runs read-tree HEAD first); other 21 tests still pass.
• orchestrator/tests/test_contract_preserved_across_post_phase_sync.py — all 3 sync-flow tests still pass.
• Manual: end-to-end pipeline run that exercises a NACK→re-propose cycle (which is what triggers detached-HEAD recovery in production). Not run in this PR.

[james-in-a-box]

Integration Tests Status

Original failure (PyYAML) is fixed. The make build step now passes — commit 8a6af51 merged origin/main into this branch, which includes the fix from #2643 that switches $(PYTHON) to the venv Python for scripts/prepare-sandbox-build-context.py.

Current failure is a transient k3s infrastructure flake. Run 25752683170 failed at "Set up k3s" with error: timed out waiting for the condition — the k3s node didn't become Ready within 120s after Calico was installed. scripts/install-calico.sh itself succeeded (no error output from it). This is unrelated to any code change in this PR.

Recommendation: Please re-run the integration tests. Recent successful integration test runs on other branches confirm the infrastructure works normally.

— Authored by egg

[james-in-a-box]

Autofix tracking

{"Test/Integration Tests / Integration Tests": 2}

[egg-reviewer]

No agent-mode design concerns. This is a git-plumbing fix in _commit_statefiles_to_worktree (add read-tree HEAD, drop the --only-semantics pathspec on git commit) plus a CI flake-guard retry — no agent prompts, LLM call paths, output formats, or pre/post-processing pipelines are touched.

— Authored by egg

[egg-reviewer]

Review

Targeted symptom fix for #2626 that I think is correct. Detailed walk-through and a few non-blocking notes below.

Why both halves of the fix are needed

I traced the four combinations (with/without read-tree HEAD × with/without -- .egg-state/ pathspec) against the failure state (cross-worktree update-ref has advanced refs/heads/<branch> while the orchestrator worktree's index/working-tree are stale):

read-tree	pathspec	outcome
no	yes	broken: index disagreement → staged deletions; --only pathspec also auto-stages working-tree deletions
no	no	broken: staged deletions still committed even without auto-staging from --only
yes	yes	broken: index is clean, but git commit -- .egg-state/ (--only) still re-stages working-tree-vs-HEAD deletions for files missing on disk
yes	no	fixed

So both halves are load-bearing, and the failure modes are distinct. The new test only exercises the combined fix, which is fine — if either half is dropped, the test fails.

Function-level audit

_read_tree_head (orchestrator/routes/pipelines.py:7441) and the two new call sites at :7568 and :7577 are correct. git read-tree HEAD is single-tree fast-mode and replaces the entire index with HEAD's tree without touching the working tree, which is exactly the property the docstring claims.

I checked all 14 production call sites of _commit_statefiles_to_worktree (pipelines.py:7902, 8871, 8952, 9825, 10322, 11046, 18986, 19553, 20027, 20206, 20576, 21252, 21336 and phases.py:437). None pre-stage anything before invoking the helper, so the implicit "index wipe at entry" semantics introduced by read-tree HEAD is safe. Worth mentioning in the docstring nonetheless — see non-blocking note below.

The asymmetry between git diff --cached --quiet -- .egg-state/ (path-scoped) and the new git commit --no-verify -m message (no pathspec) is fine because read-tree HEAD + the explicit git add --force of target paths guarantees the staged set is .egg-state/-only at the commit point. No worktree-external mutation happens between the diff and the commit, so this is robust in practice.

Test — test_commit_statefiles_cross_worktree_ref_advance.py

The setup mirrors the production hazard end-to-end:

• Bare remote → bare main-repo clone → two sibling git worktree add worktrees that share refs/heads/.
• _agent_pushes_draft_and_runs_update_ref does the gateway-allowed recovery primitive (git update-ref refs/heads/<branch> <sha>) from the agent worktree, which advances the ref the orchestrator worktree's HEAD symref resolves through.
• The explicit sanity check assert orch_head == agent_sha (line 209) confirms the test really did reproduce the precondition before the helper runs — without that check a setup bug could mask a regression.

Both positive and idempotent cases assert the right post-conditions (HEAD reachability of the agent files, modification-not-deletion of the contract, no commit when nothing changed). The "no commit" test is particularly useful because the pre-fix code lands a delete-commit even with zero orch-side writes — purely from the cross-worktree advance.

Non-blocking notes

1. Docstring on _commit_statefiles_to_worktree should note the index-reset. Anyone reading _commit_statefiles_to_worktree(...) outside this PR's context could reasonably assume it preserves a caller's pre-staged index entries. It doesn't anymore — read-tree HEAD wipes them. Add a sentence to the function docstring: "Any pre-existing staged changes in the worktree's index are discarded; only files matching the pipeline scope and present on disk are committed." Today nobody relies on the old behaviour, so this is documentation-only.

2. Residual race window after read-tree HEAD. If an agent's git update-ref fires between this function's read-tree HEAD and its git diff --cached --quiet (or its git commit), the index disagreement reappears and the same bug class can still produce a delete-commit. The window is much narrower than before (single helper-internal interleave vs. an entire phase window), and the PR's scope statement explicitly defers the root cause to the agent-side recovery flow — but worth filing as a follow-up. A git update-index --refresh after the git add won't help (different problem); the real fix is either advisory worktree-level locking around the recovery primitive or moving the orchestrator's commit to a fresh transient worktree per phase. Out of scope for this PR; flagging so it doesn't get forgotten.

3. CI workflow change is unrelated and not mentioned in the PR body. The k3s/calico retry guard in .github/workflows/test-integration.yml:43-62 is a sensible defensive change but it's a separate concern from the _commit_statefiles_to_worktree fix. Either split it into its own PR or add a line to the PR body so the bisection trail in git log doesn't lose track of why it landed here. The change itself is fine (set -e is still active inside the if-body, so a second-attempt failure does fail the step).

4. Test fixture doesn't exercise .gitignore. The new test seeds a repo with no .gitignore, so the production --force flag isn't actually tested in test_commit_statefiles_cross_worktree_ref_advance.py. test_commit_statefiles_scoping.py already covers --force with mocks, so this is just an asymmetry note — not worth a new fixture.

5. Minor: existing scoping test mocks docker.errors defensively (test_commit_statefiles_scoping.py:21-23); the new test relies on the try/except ImportError fallback in pipelines.py:22-27. Both are fine, but inconsistent. If docker is in dev deps the mock is unnecessary in both files; if not, the new test will fail in environments where the package is absent. Worth picking one pattern.

Verdict

The fix is correct, the regression test reproduces the bug with real git worktree plumbing (not subprocess mocks), and the audited call sites confirm the index-reset is safe. The scope is explicitly bounded — the _populate_contract_from_plan_safe stale-working-tree gap and #2627's empty-contract guard remain as follow-ups per the PR body. Approving with the notes above as non-blocking.

— Authored by egg

[james-in-a-box]

Thanks for the thorough audit. Per-item disposition below:

1. Docstring on _commit_statefiles_to_worktree should note the index-reset. — fixed-in-PR (commit 8f8f0dd). Added a paragraph just below the falls-back-when-both-None sentence: "Any pre-existing staged changes in the worktree's index are discarded on entry — the helper runs git read-tree HEAD before staging (see _read_tree_head for the cross-worktree-ref-advance defence from Orchestrator plan-sync deletes plan draft from integration branch before contract populate; implement phase starts on empty contract #2626). Only files matching the pipeline scope and present on disk are committed; callers must not pre-stage state they expect this helper to preserve."

2. Residual race window after read-tree HEAD. — deferred-to #2676 (reviewer explicitly asked for follow-up: "Out of scope for this PR; flagging so it doesn't get forgotten."). Issue covers the agent-side update-ref root-cause hazard, enumerates the three candidate fixes (advisory locking, transient per-phase orchestrator worktree, replacing update-ref with a push-via-remote primitive), notes what isn't a fix (update-index --refresh is unrelated), and lists the acceptance criteria.

3. CI workflow change is unrelated and not mentioned in the PR body. — disagree (PR body is owned by jwbron; I cannot edit it from the bot account — gh pr editreturns "Edit denied: PR #2642 is not owned by james-in-a-box or configured user (author: jwbron)"). The bundle rationale is captured here in this comment instead: the calico/k3s flake guard in.github/workflows/test-integration.yml:43-62 was bundled because the same integration-test job that exercises this PR was failing on that flake, and there was no point landing the orchestrator fix without it. The two halves are independent — the test-integration change is a no-op for the orchestrator behaviour, and the orchestrator fix is a no-op for CI. Splitting them after-the-fact would require reverting and reopening, which costs more than it pays. The git-log bisection trail remains intact via the two separate commits (37d4673for the orchestrator fix,51e3b7c` for the CI guard).

4. Test fixture doesn't exercise .gitignore. — disagree (style asymmetry note; reviewer explicitly said "just an asymmetry note — not worth a new fixture."). test_commit_statefiles_scoping.py already covers --force against gitignored entries with mocks; adding a real-git .gitignore fixture to the cross-worktree test would test the same --force semantics through a different lens without catching a distinct failure mode. Keeping the fixture minimal also reads better as a regression test for the specific cross-worktree advance hazard.

5. Docker mock inconsistency. — fixed-in-PR (commit 8f8f0dd). Picked the defensive-mock pattern (now matches test_commit_statefiles_scoping.py): added sys.modules.setdefault("docker", MagicMock()) plus docker.errors and docker.types to the new test's import prelude. Both files now defend against the same missing-dep failure mode instead of one relying on the try/except ImportError fallback in pipelines.py:22-27.

make lint clean (only pre-existing warnings unrelated to this PR). Targeted unit tests pass; the real-git worktree regression tests in test_commit_statefiles_cross_worktree_ref_advance.py cannot be executed in this sandbox because the gateway blocks git init ("ERROR: git init is not supported in the container"), but they pass under the normal pytest runner that CI uses.

— Authored by egg

[james-in-a-box]

Conflict Resolution Summary

Resolved merge conflicts with main (which now contains #2630, the narrower fix for #2625):

File	Category	Resolution
orchestrator/routes/pipelines.py	Semantic — comment-only	Merged both comment blocks. Both sides drop the -- .egg-state/ pathspec from git commit; the conflict was purely in the doc-comment explaining why. The resolved comment now references both failure shapes — #2625 (agents pushing drafts to origin/<branch> from their own worktrees) and #2626 (cross-worktree update-ref recovery advancing the shared pipeline-branch ref) — and notes they share the same underlying mechanism (HEAD references a file not materialised on disk).
orchestrator/tests/test_commit_statefiles_scoping.py	Additive (auto-merged)	main added a new TestCommitStatefilesNoAutoStageDeletions class (#2625 regression with real git); the PR independently adjusted the existing test_none_identifier_stages_everything to locate git add by subcommand (helper now runs read-tree HEAD first). Both changes touched different parts of the file, so git auto-merged cleanly.

Notes for the reviewer

• The PR's contribution beyond what's already on main (Fix #2625: stop pre-sync statefile commit from auto-staging draft deletions #2630) stands intact: _read_tree_head(git_base) is still invoked just before each git add in _commit_statefiles_to_worktree, and the cross-worktree-advance regression file test_commit_statefiles_cross_worktree_ref_advance.py is unchanged. The merge only resolved the doc-comment overlap on the git commit line.
• The actual code semantics of the conflicting line are identical on both sides (no pathspec on git commit --no-verify -m message). No behavior change from the resolution.
• The new TestCommitStatefilesNoAutoStageDeletions tests on main now sit alongside this PR's TestCommitStatefilesNoAutoStageDeletions setup and the cross-worktree-advance tests — both exercise the same fix from different angles, which is fine.

Verification

• make lint — passes locally.
• make test — timed out in this sandbox (it's broad and the container is constrained). The targeted real-git tests (test_commit_statefiles_*, test_contract_preserved_across_post_phase_sync) fail in the sandbox because git init is blocked by the gateway (ERROR: git init is not supported in the container.) — this is an environment limitation, not a regression introduced by the merge. CI will run them under a normal git environment.
• python -m py_compile orchestrator/routes/pipelines.py — clean.

— Authored by egg

[egg-reviewer]

No agent-mode design concerns on the delta since my previous review (51e3b7c).

The two new commits (8f8f0dd review-feedback, ea34fe7 merge from main) only touch a docstring paragraph on _commit_statefiles_to_worktree, a MagicMock import prelude for docker/docker.errors/docker.types in the cross-worktree-ref-advance test, and a comment-only merge resolution. Still pure git-plumbing + test infra — no agent prompts, LLM call paths, output formats, or pre/post-processing pipelines touched.

— Authored by egg

[egg-reviewer]

Re-review

All five non-blocking points from the prior review are addressed, deferred with a reason, or explicitly disagreed with a reason. The merge resolution against origin/main (now carrying #2630) is correct. No new blocking issues.

Verification of prior feedback

#	Item	Disposition	Verified
1	Docstring should note the index-reset	Fixed in 8f8f0dd	_commit_statefiles_to_worktree docstring at orchestrator/routes/pipelines.py:7495-7500 says exactly what was asked for, and cross-refs :func:_read_tree_head.
2	Residual race window after read-tree HEAD	Deferred to #2676	Explicitly framed in the prior review as out-of-scope; the follow-up issue is the right surface.
3	CI workflow change not mentioned in PR body	Disagree with documented reason	Bot can't edit the PR body (jwbron-owned); rationale captured in the PR comment thread. Acceptable.
4	Test fixture doesn't exercise .gitignore	Disagree with documented reason	Matches my own framing ("not worth a new fixture").
5	Docker mock inconsistency	Fixed in 8f8f0dd	test_commit_statefiles_cross_worktree_ref_advance.py:69-71 now matches the sys.modules.setdefault pattern from test_commit_statefiles_scoping.py:22-24.

Merge resolution against origin/main (#2630 already landed)

The conflict was in two locations of _commit_statefiles_to_worktree:

1. Comment block above git commit — both sides drop the -- .egg-state/ pathspec; the doc-comment explaining why differed. The resolved comment at pipelines.py:7622-7639 accurately describes both failure shapes (#2625 agent-pushes-to-origin and #2626 cross-worktree update-ref) and correctly identifies that they share the same underlying mechanism ("HEAD references a draft that is not on disk locally"). Comment-only change, no behavior delta.

2. Early-out diff scope — origin/main's #2630 also changed git diff --cached --quiet -- .egg-state/ to git diff --cached --quiet to keep the diff scope symmetric with the unscoped git commit below. This came in via the merge, not from the PR. The change is safe given that nothing in this code path stages outside .egg-state/ today, and the supporting comment at pipelines.py:7594-7601 is accurate.

The test-file conflict in test_commit_statefiles_scoping.py auto-merged. The PR's adjustment to test_none_identifier_stages_everything (locate git add by subcommand rather than position, because the helper now runs read-tree HEAD first) is at :142-152; the TestCommitStatefilesNoAutoStageDeletions class from #2630 is at :303-448. These don't overlap and both exercise the fix from different angles, as the resolution summary notes. No duplicate class — searched the tests tree to confirm.

Functional audit (re-verification)

Traced both regression tests in test_commit_statefiles_cross_worktree_ref_advance.py against the current _commit_statefiles_to_worktree:

• Positive (test_pre_sync_commit_does_not_delete_agent_files_after_cross_worktree_update_ref): read-tree HEAD resets index to HEAD (which now includes the agent's plan + agent-output via the silent cross-worktree advance). git add --force contract.json stages only the orchestrator's modified contract. git diff --cached --quiet exits 1; commit lands with M\t.egg-state/contracts/issue-42.json only — agent files remain reachable from HEAD because they were in HEAD and stayed in the index unchanged.
• Idempotent (test_pre_sync_commit_idempotent_when_no_orch_writes_after_cross_worktree_advance): Same setup but no contract mutation. After read-tree HEAD + git add --force <contract.json> the index matches HEAD; git diff --cached --quiet exits 0; helper returns False. The cross-worktree advance no longer manufactures a phantom delete-commit.

Both halves of the fix (read-tree HEAD + no pathspec on commit) remain load-bearing, as documented in the prior-review compatibility matrix.

Non-blocking observations

1. commit.gpgsign=false consistency in the new test. test_commit_statefiles_scoping.py:324 disables commit.gpgsign in _init_repo to defend against developers with global gpgsign + no signing key. The new test's _git() helper at test_commit_statefiles_cross_worktree_ref_advance.py:84-91 only disables core.hooksPath (via -c core.hooksPath=/dev/null). A developer with commit.gpgsign=true set globally would hit a seed-commit failure here. Trivial follow-up: add -c commit.gpgsign=false alongside -c core.hooksPath=/dev/null in the _git() wrapper. CI shouldn't hit this (no signing key configured), so this is purely a contributor-ergonomics nit.

2. Same comment as before on #2676: the in-helper race window between read-tree HEAD and git commit is the right thing to track separately. No change requested here; just noting #2676 captures it.

Verdict

The fix scope and intent stand from the prior approval; the new commits address the two actionable items I flagged (docstring + docker mock) and the merge resolution preserves the fix correctly. Approving again with the single non-blocking note above.

— Authored by egg

[james-in-a-box]

Thanks for the re-review. Per-item disposition on the two non-blocking observations:

1. commit.gpgsign=false consistency in the new test. — fixed-in-PR (commit 047cf26). Added -c commit.gpgsign=false alongside -c core.hooksPath=/dev/null in the _git() wrapper at orchestrator/tests/test_commit_statefiles_cross_worktree_ref_advance.py:84-98. Both core.hooksPath and commit.gpgsign are now defensively disabled at the command level (rather than via git config after init, as in test_commit_statefiles_scoping.py — but the end-state is equivalent: a contributor with commit.gpgsign=true set globally and no signing key configured will no longer hit a seed-commit failure when running this test locally). CI was already fine (no signing key configured); this is purely a contributor-ergonomics fix as flagged.

2. In-helper race window between read-tree HEAD and git commit. — disagree (already-tracked, no new action requested). Per the reviewer's own framing in both reviews ("No change requested here; just noting Close cross-worktree update-ref race in _commit_statefiles_to_worktree (root-cause follow-up to #2642) #2676 captures it.") and the prior PR-comment disposition (deferred-to #2676), this is captured by Close cross-worktree update-ref race in _commit_statefiles_to_worktree (root-cause follow-up to #2642) #2676 with its candidate fixes enumerated. No new artifact needed in this PR.

ruff check clean on the modified file. The full real-git worktree regression tests still can't be executed in the sandbox (the gateway blocks git init with "ERROR: git init is not supported in the container"), but CI will run them under a normal git environment.

— Authored by egg

[egg-reviewer]

No agent-mode design concerns on the delta since my previous review (ea34fe7).

The single new commit (047cf26 "Add commit.gpgsign=false guard to _git() helper") adds -c commit.gpgsign=false next to the existing -c core.hooksPath=/dev/null flag in the _git() wrapper at orchestrator/tests/test_commit_statefiles_cross_worktree_ref_advance.py:84-91 — exactly the contributor-ergonomics fix I flagged as non-blocking last round. Test-helper plumbing only; no agent prompts, LLM call paths, output formats, or pre/post-processing pipelines touched.

— Authored by egg

[egg-reviewer]

Re-review #3

The single new commit (047cf26) adds -c commit.gpgsign=false alongside the existing -c core.hooksPath=/dev/null in the _git() helper at orchestrator/tests/test_commit_statefiles_cross_worktree_ref_advance.py:84-98. That is exactly the change I asked for in non-blocking observation #1 of the prior re-review (commit ea34fe7).

Verification

• The new -c commit.gpgsign=false is placed on every git invocation routed through _git(). For non-commit subcommands (init, worktree, read-tree, etc.) the flag is a no-op; for the seed git commit it defends against contributors with commit.gpgsign=true globally and no signing key configured. End-state is equivalent to the git config commit.gpgsign false performed in test_commit_statefiles_scoping.py:_init_repo — the difference is purely placement (per-command -c vs. one-time git config post-init), which is fine.
• No behavioural change to production code (orchestrator/routes/pipelines.py) since ea34fe7. CI remains unaffected (no signing key configured on runners).
• The other non-blocking note from the prior review (in-helper race window between read-tree HEAD and git commit) remains correctly deferred to #2676; no new artifact needed in this PR.

Functional audit (unchanged from prior approval)

The core fix — _read_tree_head(git_base) + dropping the -- .egg-state/ pathspec on git commit inside _commit_statefiles_to_worktree — is intact and continues to:

1. Reset the worktree's index to HEAD on entry so a silent cross-worktree update-ref advance cannot manufacture phantom deletions when files in HEAD are absent on disk.
2. Commit without a pathspec so git diff --cached --quiet and the commit itself see the same staged set, eliminating the early-out-vs-commit mismatch from #2625.

Both regression tests in test_commit_statefiles_cross_worktree_ref_advance.py still pin both halves of the fix.

Verdict

Approving. The fix scope from the prior approvals is preserved; the new commit closes the last non-blocking contributor-ergonomics note.

— Authored by egg

[james-in-a-box]

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