fix: add tree hash and patch ID checkpoint linkage fallback by peyton-alt · Pull Request #840 · entireio/cli

peyton-alt · 2026-04-03T00:25:50Z

Summary

Store a narrow, Git-native linkage block in checkpoint metadata so the web has limited fallback signals when history rewrites strip the Entire-Checkpoint trailer.

add checkpoint-level linkage metadata with tree_hash and patch_id
keep the existing active-session revert/cherry-pick trailer behavior, but only reuse an existing LastCheckpointID
avoid generating new checkpoint IDs during sequence operations, since those commits are not condensed immediately

Scope

This PR is intentionally narrow.

It does not implement full automatic relinking across all rewrite scenarios, and it does not add custom derived signals like files_changed_hash or session_files_hash.

The supported fallback signals are:

tree_hash for message-only rewrites where the tree is unchanged
patch_id for clean rebases or cherry-picks where the diff content is unchanged

Why this shape

The broader multi-signal design implied server-side indexing and reconciliation work that this PR does not provide.

This branch keeps only the cheap, Git-native fallback signals that are defensible today, while the real active-session rewrite tracking work moves to the CLI (post-rewrite) in a separate follow-up.

Sequence-operation behavior

prepare-commit-msg can still add a trailer during agent-driven revert/cherry-pick when a session is ACTIVE, but it now only reuses an existing LastCheckpointID.

That matters because post-commit still skips condensation while the sequence operation is in progress. Reusing an existing checkpoint ID preserves a valid link; minting a fresh one would leave a dangling Entire-Checkpoint trailer on the commit.

Testing

Passed:

GOCACHE=/tmp/go-build go test ./cmd/entire/cli/strategy -run 'TestShadowStrategy_(PrepareCommitMsg_(AgentRevertReusesLastCheckpointID|AgentRevertWithoutCheckpointIDSkipped|UserRevertSkipped)|PostCommit_LinkagePopulated)' -count=1
GOCACHE=/tmp/go-build go test ./cmd/entire/cli/checkpoint ./cmd/entire/cli/gitops -count=1
GOCACHE=/tmp/go-build GOLANGCI_LINT_CACHE=/tmp/golangci-lint golangci-lint run ./cmd/entire/cli/strategy ./cmd/entire/cli/checkpoint ./cmd/entire/cli/gitops

Included coverage verifies:

linkage is written at the checkpoint summary level
both tree_hash and patch_id are populated in the condensation path
clean rebases keep a stable patch_id
agent-driven revert reuses an existing checkpoint trailer when available
agent-driven revert skips trailer injection when no existing checkpoint ID can be reused
user-driven revert still skips trailer injection

Copilot

Pull request overview

Stores a commit’s git tree hash in checkpoint metadata during condensation so the web side can re-link checkpoints after history rewrites that drop the Entire-Checkpoint trailer, and tweaks prepare-commit-msg behavior so agent-driven revert/cherry-pick operations still get checkpoint trailers when a session is active.

Changes:

Add tree_hash to committed checkpoint metadata (CommittedMetadata, WriteCommittedOptions) and populate it during PostCommit condensation from the HEAD commit’s tree hash.
Allow prepare-commit-msg to proceed during git sequence operations (revert/cherry-pick/rebase) when an ACTIVE session exists in the current worktree; keep skipping when no active session.
Add unit tests for tree_hash persistence and the new revert trailer behavior split by agent-active vs user/manual.

Reviewed changes

Copilot reviewed 7 out of 7 changed files in this pull request and generated 1 comment.

Show a summary per file

File	Description
cmd/entire/cli/strategy/manual_commit_test.go	Adds tests ensuring agent revert gets a trailer when session is ACTIVE and user revert is skipped when not active.
cmd/entire/cli/strategy/manual_commit_session.go	Adds helper to detect whether any session in the current worktree is ACTIVE.
cmd/entire/cli/strategy/manual_commit_hooks.go	Adjusts PrepareCommitMsg sequence-operation skip logic; passes commit tree hash into condensation options.
cmd/entire/cli/strategy/manual_commit_condensation.go	Threads `treeHash` through condensation options into committed checkpoint write options.
cmd/entire/cli/checkpoint/committed.go	Writes `TreeHash` into per-session committed metadata.json.
cmd/entire/cli/checkpoint/checkpoint.go	Extends checkpoint option/metadata structs to include `TreeHash` serialized as `tree_hash`.
cmd/entire/cli/checkpoint/checkpoint_test.go	Adds coverage that `tree_hash` is written and read back from committed metadata.

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Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

Add checkpoint linkage preservation after history rewrites (#840) and fail-closed content detection in prepare-commit-msg (#826). Update release date to 2026-04-03. Signed-off-by: Paulo Gomes <paulo@entire.io> Assisted-by: Claude Opus 4.6 <noreply@anthropic.com> Entire-Checkpoint: 0154164ac0f9

When an agent runs git revert or cherry-pick as part of its work, the commit should be checkpointed. Previously prepare-commit-msg unconditionally skipped during sequence operations, making the agent's work invisible to Entire. Now checks for active sessions: if an agent session is ACTIVE, the operation is agent-initiated and gets a trailer. If no active session, it's user-initiated and is skipped as before. Part of fix for #834. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com> Entire-Checkpoint: 85df9ac94bc7

Add tree_hash field to committed checkpoint metadata. Records the git tree hash of the commit being condensed, enabling fallback checkpoint lookup by tree hash when the Entire-Checkpoint trailer is stripped by git history rewrites (rebase, filter-branch, amend). Part of fix for #834. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com> Entire-Checkpoint: 77773a25069e

- Add debug logging to hasActiveSessionInWorktree error paths - Remove unrelated files (greetings.md, agent configs) from PR Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com> Entire-Checkpoint: bacd9b68b1c0

Define content-based linkage signals (tree_hash, patch_id, files_changed_hash, session_files_hash) for re-linking checkpoints after git history rewrites. Stored at checkpoint level, not per-session. Part of fix for #834. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com> Entire-Checkpoint: 4661e8c50610

Needed by linkage signal tests that verify patch ID stability across rebase. Part of fix for #834. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com> Entire-Checkpoint: 4129c08c80b0

ComputePatchID: git patch-id of the commit diff, survives rebase. ComputeFilesChangedHash: SHA256 of sorted file:blob pairs, survives rebase even with conflicts in non-agent files. Uses single git ls-tree call for all files (O(1) subprocess). Part of fix for #834. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com> Entire-Checkpoint: c100b592e3a0

Replace per-session TreeHash with checkpoint-level LinkageMetadata containing tree_hash, patch_id, files_changed_hash, and session_files_hash. Computed in PostCommit handlers, passed through condenseOpts to CondenseSession, written to CheckpointSummary on entire/checkpoints/v1. Part of fix for #834. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com> Entire-Checkpoint: 75ce05cfe11b

Verify LinkageMetadata is stored in CheckpointSummary and readable. Also verify nil linkage is omitted (backward compat with old checkpoints). Part of fix for #834. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com> Entire-Checkpoint: 10dae87903d7

gofmt stripped nolint directives from capabilities.go. Restore from main. Add encoding/hex import for ComputeFilesChangedHash. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com> Entire-Checkpoint: c26d3dce1d32

- Restore nolint:ireturn on capabilities.go (gofmt stripped them) - Set user.name/email in gitops initTestRepo for CI compatibility (git rebase fails without repo-level config on CI runners) Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com> Entire-Checkpoint: f1ca53b63c79

- Add omitempty to all LinkageMetadata JSON tags for consistency - Return error for malformed git ls-tree lines instead of silent skip - Compute commit-level linkage once (not per-session) via baseLinkage cache; only SessionFilesHash varies per session - Add code comment explaining deferred condensation for agent reverts - Add integration test verifying full linkage pipeline (PostCommit → condensation → ReadCommitted with all four signals populated) Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com> Entire-Checkpoint: e3539c5bfa31

- Replace unreachable Fields/len guard with strings.Cut in ComputePatchID - Use logCtx variable in linkageForSession for logging consistency - Use strings.TrimSpace in revParse test helper instead of raw byte slice Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com> Entire-Checkpoint: 91b06c4aabdb

Entire-Checkpoint: 5f47003ea308

Entire-Checkpoint: 391cbda054cc

Narrow checkpoint linkage to tree hash and patch ID

Soph

Claude Review Suggestions:

Misleading field name IsRebaseInProgress at cmd/entire/cli/strategy/manual_commit_hooks.go:1098 — now also covers cherry-pick and revert. Rename to IsSequenceOperationInProgress or add a comment.
PatchID unstable under conflict-resolved rebases — git patch-id --stable changes if the user resolves conflicts during rebase. Add a one-line doc note on PatchID in LinkageMetadata.
Missing cherry-pick test for PrepareCommitMsg with an active session (revert is covered thoroughly, cherry-pick is symmetric).
Duplicate helpers in cmd/entire/cli/gitops/diff_test.go (revParse, gitCheckout, gitRebase) shadow the new testutil helpers added in this branch — maybe replace them?
Document "same ID from two sessions = ambiguous" in singleReusableCheckpointID — the behavior is correct, just non-obvious.

Copilot AI review requested due to automatic review settings April 3, 2026 00:25

peyton-alt requested a review from a team as a code owner April 3, 2026 00:25

Copilot started reviewing on behalf of peyton-alt April 3, 2026 00:26 View session

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peyton-alt added a commit that referenced this pull request Apr 3, 2026

docs: add changelog entries for #826 and #840

c8ffa52

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

Copilot AI mentioned this pull request Apr 3, 2026

docs: add changelog entries for #826 and #840 #841

Closed

pjbgf mentioned this pull request Apr 3, 2026

docs: update v0.5.3 changelog with additional bug fixes #843

Merged

peyton-alt marked this pull request as draft April 7, 2026 05:49

peyton-alt force-pushed the peyton/ent-834-tree-hash-checkpoint-linkage branch from 7b9d87d to 8302847 Compare April 7, 2026 06:17

peyton-alt changed the title ~~fix: store tree hash in checkpoint metadata for linkage resilience~~ feat: multi-signal checkpoint linkage for resilience across git rewrites Apr 7, 2026

peyton-alt force-pushed the peyton/ent-834-tree-hash-checkpoint-linkage branch 3 times, most recently from 0dfcba0 to 703bd67 Compare April 7, 2026 23:55

peyton-alt marked this pull request as ready for review April 8, 2026 00:17

Soph force-pushed the main branch from cb49513 to 2c2cd25 Compare April 8, 2026 13:47

peyton-alt force-pushed the peyton/ent-834-tree-hash-checkpoint-linkage branch from 703bd67 to fa8cbb5 Compare April 10, 2026 01:34

peyton-alt changed the title ~~feat: multi-signal checkpoint linkage for resilience across git rewrites~~ fix: checkpoint linkage survives git rebase and history rewrites Apr 10, 2026

peyton-alt and others added 9 commits April 9, 2026 22:08

fix: add debug logging + remove unrelated files

8490173

- Add debug logging to hasActiveSessionInWorktree error paths - Remove unrelated files (greetings.md, agent configs) from PR Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com> Entire-Checkpoint: bacd9b68b1c0

test: add GitRevParse, GitCheckout, GitRebase testutil helpers

cce8e64

Needed by linkage signal tests that verify patch ID stability across rebase. Part of fix for #834. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com> Entire-Checkpoint: 4129c08c80b0

peyton-alt and others added 3 commits April 9, 2026 22:08

peyton-alt force-pushed the peyton/ent-834-tree-hash-checkpoint-linkage branch from fa8cbb5 to 7cfa919 Compare April 10, 2026 05:09

peyton-alt and others added 4 commits April 13, 2026 15:14

Narrow checkpoint linkage to tree hash and patch ID

fcb4e4a

Entire-Checkpoint: 5f47003ea308

Clarify commit-level linkage caching

531a4d1

Entire-Checkpoint: 391cbda054cc

Merge pull request #945 from entireio/peyton/ent-834-linkage-cleanup

bc8c48a

Narrow checkpoint linkage to tree hash and patch ID

Fix sequence-operation checkpoint trailer reuse

8571f4d

peyton-alt changed the title ~~fix: checkpoint linkage survives git rebase and history rewrites~~ fix: add tree hash and patch ID checkpoint linkage fallback Apr 15, 2026

Merge origin/main into peyton/ent-834-tree-hash-checkpoint-linkage

da5cea2

peyton-alt force-pushed the peyton/ent-834-tree-hash-checkpoint-linkage branch from 7487fcf to da5cea2 Compare April 15, 2026 05:30

peyton-alt added 2 commits April 14, 2026 22:42

Tighten sequence-operation checkpoint reuse

63f3c05

Merge origin/main into peyton/ent-834-tree-hash-checkpoint-linkage

f2fb5e7

Soph reviewed Apr 15, 2026

View reviewed changes

peyton-alt added 2 commits April 15, 2026 12:14

Tighten sequence-operation linkage docs and tests

1334c5e

Merge origin/main into peyton/ent-834-tree-hash-checkpoint-linkage

2b2cb11

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fix: add tree hash and patch ID checkpoint linkage fallback#840

fix: add tree hash and patch ID checkpoint linkage fallback#840
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Summary

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Why this shape

Sequence-operation behavior

Testing

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