fix: subagent file modifications invisible to checkpoint detection (ENT-297) by khaong · Pull Request #323 · entireio/cli

khaong · 2026-02-13T12:42:10Z

Summary

Fixes subagent file modifications being invisible to checkpoint detection. When Claude Code delegates work to subagents via the Task tool, file changes made by those subagents were not tracked, causing:

Missing checkpoints at Stop (subagent-only changes → totalChanges=0)
Missing checkpoint trailers on mid-session commits
Incomplete file lists in condensed checkpoint metadata
Failed PostCommit condensation for mid-subagent commits (transcript data unavailable)

Changes

ExtractAllModifiedFiles() — new function that scans both main and subagent transcripts (agent-<id>.jsonl) for Write/Edit/NotebookEdit tool calls
Stop hook — uses ExtractAllModifiedFiles so checkpoints aren't skipped when only subagents modify files
sessionHasNewContentFromLiveTranscript — augmented with subagent transcript scanning for mid-session commit detection
Shared helper extractModifiedFilesFromLiveTranscript — consolidates 3 duplicated code blocks (main transcript extraction + subagent augmentation + path normalization)
extractSessionDataFromLiveTranscript — uses shared helper so condensed checkpoints include subagent files
PostCommit ACTIVE sessions — trusts PrepareCommitMsg's trailer validation instead of re-analyzing transcripts (unreliable when subagents are still running at commit time)
Removed sessionHasNewContentInCommittedFiles — now unused after the PostCommit simplification

Key insight

At PostCommit time during a mid-subagent commit, subagent transcript data is unavailable: the main transcript has no tool_result with agentId: yet, and subagent files may still be in-flight. Since PrepareCommitMsg already validates the trailer (unconditionally for no-TTY/agent commits, via content detection for TTY/human commits), PostCommit trusts that decision for ACTIVE sessions rather than re-validating.

Fixes ENT-297

Test plan

Unit tests for ExtractAllModifiedFiles (4 cases: includes subagent files, deduplicates, no subagents, subagent-only changes)
Unit test for sessionHasNewContentFromLiveTranscript with subagent-only modifications
Unit test for PostCommit ACTIVE session always condensing
Integration test TestHookRunner_SimulateStop_SubagentOnlyChanges (both strategies)
Manual test: subagent commit → trailer added → checkpoint created
Full CI suite passes (mise run fmt && mise run lint && mise run test:ci)

🤖 Generated with Claude Code

Copilot

Pull request overview

This PR fixes ENT-297 by ensuring checkpoint detection includes file modifications performed by Claude Code subagents (spawned via the Task tool), so turns aren’t skipped when only subagents write/edit files.

Changes:

Added claudecode.ExtractAllModifiedFiles() to aggregate modified files across main + subagent transcripts.
Updated Claude Code stop hook (commitWithMetadata) and mid-session “new content” detection to include subagent transcripts.
Added unit and integration tests to cover subagent-only modification scenarios.

Reviewed changes

Copilot reviewed 9 out of 9 changed files in this pull request and generated 5 comments.

Show a summary per file

File	Description
cmd/entire/cli/agent/claudecode/transcript.go	Adds `ExtractAllModifiedFiles()` to collect modified files from main + subagent transcripts.
cmd/entire/cli/hooks_claudecode_handlers.go	Stop hook now uses `ExtractAllModifiedFiles()` for subagent-aware modified-file detection.
cmd/entire/cli/strategy/manual_commit_hooks.go	Mid-session commit detection now checks subagent transcripts for Claude Code sessions.
cmd/entire/cli/agent/claudecode/transcript_test.go	Adds unit tests for `ExtractAllModifiedFiles()` (subagent inclusion + dedupe cases).
cmd/entire/cli/strategy/mid_turn_commit_test.go	Adds test ensuring subagent-only changes are detected as “new content.”
cmd/entire/cli/integration_test/hooks_test.go	Adds integration regression test for stop-hook checkpointing when only subagents modify files.
cmd/entire/cli/strategy/registry.go	Updates `//nolint:ireturn` rationale comment.
cmd/entire/cli/strategy/manual_commit.go	Updates `//nolint:ireturn` rationale comment.
cmd/entire/cli/strategy/auto_commit.go	Updates `//nolint:ireturn` rationale comment.

cmd/entire/cli/agent/claudecode/transcript.go

cmd/entire/cli/integration_test/hooks_test.go

cmd/entire/cli/hooks_claudecode_handlers.go

cmd/entire/cli/strategy/manual_commit_hooks.go

…gents This function extracts modified file paths from both the main transcript and any subagent transcripts spawned via the Task tool. It follows the same pattern as CalculateTotalTokenUsage: parse once, extract agent IDs, read subagent transcripts, and merge results with deduplication. This is the foundation for fixing ENT-297 where subagent-only file changes were invisible to checkpointing. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com> Entire-Checkpoint: 732abe6dd3e4

Replace extractModifiedFiles (main transcript only) with claudecode.ExtractAllModifiedFiles which also parses subagent transcripts. This fixes the core bug where subagent-only file changes produced totalChanges=0, causing checkpoints to be skipped. Falls back to main-transcript-only extraction on error. Also reuses the subagentsDir variable for token usage calculation to avoid redefinition. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com> Entire-Checkpoint: 732abe6dd3e4

…difications The PrepareCommitMsg hook's live transcript check only scanned the main transcript via ExtractModifiedFilesFromOffset, missing file changes made by subagents spawned via the Task tool. When the main transcript contained only Task calls (no direct Write/Edit), modifiedFiles was empty and the function returned false -- causing missing checkpoint trailers on commits that included subagent-written files. After the existing main transcript scan, also call claudecode.ExtractAllModifiedFiles which parses both the main and subagent transcripts, picking up Write/Edit tool calls from subagent files. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com> Entire-Checkpoint: 732abe6dd3e4

…-297) Verify that the Stop hook creates checkpoints when only subagents modify files. The test constructs a main transcript with only a Task tool call and a subagent transcript with Write tool calls, then confirms both auto-commit and manual-commit strategies detect the changes via ExtractAllModifiedFiles. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com> Entire-Checkpoint: 732abe6dd3e4

- Add logging.Debug when ExtractAllModifiedFiles errors in sessionHasNewContentFromLiveTranscript (was silently swallowed) - Fix AddTaskToolResult to produce "agentId: <id>" format matching real Claude Code transcripts (was "Task completed by agent <id>") - Use AddTaskToolResult in integration test instead of reaching into TranscriptBuilder internals Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com> Entire-Checkpoint: 1facd4391816

Three functions duplicated the same pattern: extract modified files from the main transcript, augment with subagent transcripts, normalize paths. Consolidate into extractModifiedFilesFromLiveTranscript(state, offset) and two thin wrappers (extractFilesFromLiveTranscript for carry-forward, extractNewModifiedFilesFromLiveTranscript for content detection). Also wires subagent file extraction into extractFilesFromLiveTranscript (carry-forward) and sessionHasNewContentInCommittedFiles (PostCommit ACTIVE sessions) which were missing it. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com> Entire-Checkpoint: fc1317d7f797

When condensing a mid-session commit (no shadow branch), FilesTouched was extracted only from the main transcript. Subagent-modified files were missed, causing the condensed checkpoint to have incomplete file lists. Use the shared extractModifiedFilesFromLiveTranscript helper which includes subagent transcripts. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com> Entire-Checkpoint: e91ff0dab977

For ACTIVE sessions in PostCommit, always set hasNew=true instead of re-validating via transcript analysis. PrepareCommitMsg already validates the trailer (unconditionally for no-TTY/agent commits, via content detection for TTY/human commits). Transcript-based re-validation is unreliable because subagent transcripts may not be available at PostCommit time (subagent still running). Removes sessionHasNewContentInCommittedFiles which is now unused. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com> Entire-Checkpoint: f20127b19334

khaong · 2026-02-15T06:44:24Z

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Copilot

Pull request overview

Copilot reviewed 12 out of 12 changed files in this pull request and generated no new comments.

cmd/entire/cli/strategy/manual_commit_hooks.go

For Claude Code agents, skip the generic ExtractModifiedFilesFromOffset call and go directly to ExtractAllModifiedFiles, which parses the main transcript and subagent transcripts in one pass. Previously both were called, parsing the main transcript twice. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com> Entire-Checkpoint: 184069756ffc

khaong · 2026-02-15T08:08:24Z

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Copilot AI review requested due to automatic review settings February 13, 2026 12:42

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This was referenced Feb 13, 2026

bufio.Scanner 10MB token limit may truncate large transcript lines #328

Open

ExtractSpawnedAgentIDs misses subagents spawned before startLine offset #329

Open

khaong force-pushed the alex/ent-297-fix-subagent-only-changes-checkpointing branch from 2d26295 to 97fb2a9 Compare February 15, 2026 03:32

khaong changed the base branch from main to soph/one-to-one-checkpoints February 15, 2026 03:33

khaong and others added 8 commits February 15, 2026 17:22

khaong force-pushed the alex/ent-297-fix-subagent-only-changes-checkpointing branch from 017c468 to cdc5c7e Compare February 15, 2026 06:23

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cmd/entire/cli/strategy/manual_commit_hooks.go Show resolved Hide resolved

khaong marked this pull request as ready for review February 15, 2026 08:08

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Merge branch 'soph/one-to-one-checkpoints' into alex/ent-297-fix-suba…

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Base automatically changed from soph/one-to-one-checkpoints to main February 15, 2026 09:13

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fix: subagent file modifications invisible to checkpoint detection (ENT-297)#323

fix: subagent file modifications invisible to checkpoint detection (ENT-297)#323
khaong wants to merge 11 commits intomainfrom
alex/ent-297-fix-subagent-only-changes-checkpointing

khaong commented Feb 13, 2026 •

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