fix: isolate summarization subprocess from git repo (ENT-242, ENT-243)

[khaong]

Summary

• ENT-242: Claude Code's summarization subprocess (claude --print) was polluting the worktree index with phantom entries from its internal plugin cache (e.g., tests/claude-code/README.md with blob SHA that doesn't exist in the object store), causing fatal: unable to read <sha> errors on subsequent git status calls. Fix isolates the subprocess by running from os.TempDir(), stripping all GIT_* env vars, and using empty --setting-sources.
• ENT-243: Generated summaries were silently dropped during condensation because writeSessionToSubdirectory() was missing Summary: opts.Summary in the CommittedMetadata struct literal.

Root cause investigation

The original theory (go-git's worktree.Status() rewriting the index) was wrong — Status() only reads the index, never writes it. The actual cause was the claude --print subprocess inheriting the git hook environment (GIT_DIR), which let Claude Code's internal git operations (plugin cache, context gathering) write phantom entries into the worktree index.

Confirmed by:

1. Replacing claude --print with a 15s sleep → index stays clean
2. Running claude --print from tmpdir without GIT_* env vars → index stays clean
3. Running claude --print from tmpdir WITH GIT_* env vars → index still corrupted

Test plan

• mise run fmt && mise run lint && mise run test:ci passes
• Manual testing: 3 consecutive condensation commits with clean index checksums (before/after md5 match)
• Verify summary field appears in condensed metadata.json

🤖 Generated with Claude Code

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Note

Medium Risk
Touches checkpoint metadata persistence and changes how the summarization subprocess is executed (working directory and environment), which could affect summary generation behavior and any setups relying on inherited git/config state.

Overview
Prevents Claude CLI summarization (claude --print) from polluting or discovering the caller’s git repo by disabling settings loading (--setting-sources ""), running the subprocess from os.TempDir(), and stripping all inherited GIT_* environment variables.

Fixes a checkpoint persistence regression by actually writing WriteCommittedOptions.Summary into the session-level metadata.json, and adds regression tests covering both summary persistence and the new git-isolation behavior.

^{Written by Cursor Bugbot for commit e23db7a. This will update automatically on new commits. Configure here.}

[Copilot]

Pull request overview

This PR addresses two condensation/summarization issues in Entire CLI: it isolates the Claude CLI summarization subprocess from the user’s git repository to prevent index corruption (ENT-242), and ensures generated summaries are persisted into committed session metadata (ENT-243).

Changes:

• Run claude --print from os.TempDir() and strip all GIT_* environment variables to prevent the subprocess from discovering/modifying the parent repo.
• Use an empty --setting-sources value to avoid loading user/project/local settings during summarization.
• Persist Summary into CommittedMetadata when writing session-level metadata.json.

Reviewed changes

Copilot reviewed 2 out of 2 changed files in this pull request and generated 2 comments.

File	Description
cmd/entire/cli/summarize/claude.go	Isolates the Claude summarization subprocess via temp working dir + stripped git env to prevent index pollution.
cmd/entire/cli/checkpoint/committed.go	Fixes omission so opts.Summary is written into session-level committed metadata.