Only first commit per session gets Entire-Checkpoint trailer; subsequent commits silently skipped

Summary

When using entire configure --agent claude-code with the manual-commit strategy, only the first commit per turn gets the Entire-Checkpoint trailer. Subsequent commits within the same turn, and all commits in later turns, are silently skipped — no trailer is added, no checkpoint is created, and no error is logged.

This breaks the documented "Multiple checkpoints, single session" workflow described at https://docs.entire.io/web/sessions:

"A developer might have a single session running in a terminal while creating multiple commits throughout that session and thereby creating multiple checkpoints. Entire will match up these checkpoints to the single session."

Environment

• Entire CLI: 0.5.1 (d46fdc24)
• OS: Linux (Manjaro)
• Agent: claude-code
• Strategy: manual-commit
• Git hooks path: .husky/_ (via core.hooksPath)

Observed behavior

Prompt-by-prompt breakdown

1. Prompt 1 — generated a single commit 7917a85. ✅ Linked to session with checkpoint 1754c2af9609.

2. Prompt 2 — generated 3 commits while Claude Code was working:

   • 0dd88fa ✅ Linked to session with checkpoint 07386117e61f (first commit of this turn)
   • abb3213 ❌ No Entire-Checkpoint trailer
   • e1f6802 ❌ No Entire-Checkpoint trailer

3. Prompt 3 (same session, new turn) — generated 1 commit:

   • 482a585 ❌ No Entire-Checkpoint trailer

Pattern: Only the first commit ever made in a turn gets linked. After the post-commit hook runs for that first commit, all subsequent commits in the session are orphaned.

Dashboard view

Only 2 out of 5 commits show the "Claude Code" badge and checkpoint:

#	Commit	Message	Linked?
5	482a585	chore: clean up dependencies...	❌ No trailer
4	e1f6802	feat: integrate Openfort + Viem...	❌ No trailer
3	abb3213	refactor: remove Particle Network...	❌ No trailer
2	0dd88fa	style: format entire codebase...	✅ checkpoint 07386117e61f
1	7917a85	docs: add v0.1.0 status report...	✅ checkpoint 1754c2af9609

Root cause (from .entire/logs/entire.log)

The post-commit hook deletes the shadow branch after condensing the session. When the next commit happens, prepare-commit-msg cannot find the shadow branch, and silently produces no trailer.

Sequence from the log:

# Prompt 1, commit 1 (7917a85) — works
prepare-commit-msg: agent commit trailer added   (checkpoint: 1754c2af9609)
session condensed
shadow branch deleted                            ← shadow branch gone

# Prompt 2, commit 1 (0dd88fa) — works (shadow branch recreated between turns)
prepare-commit-msg: agent commit trailer added   (checkpoint: 07386117e61f)
session condensed
sessionHasNewContent: no shadow branch, checking live transcript
shadow branch deleted                            ← shadow branch gone again

# Prompt 2, commits 2-3 (abb3213, e1f6802) — NO prepare-commit-msg log entries at all
# The hook runs but entire silently exits without adding a trailer
# At turn-end, entire notices HEAD moved:
updated session base commit (HEAD changed during session), new_base: e1f6802

# Prompt 3, commit 1 (482a585) — also not linked
# No prepare-commit-msg log entry, shadow branch not available

The key gap: between 23:39:00 (shadow branch entire/7917a85-e3b0c4 deleted after commit 0dd88fa) and 23:47:42 (turn-end), two more commits were made with zero prepare-commit-msg activity in the log. The hook script pipes stderr to /dev/null (2>/dev/null || true), so any errors from entire hooks git prepare-commit-msg are silently swallowed.

No workaround available

We checked the available CLI commands (entire clean, entire reset, entire doctor) — none of them address this issue:

• entire clean — only removes orphaned data, doesn't recreate shadow branches
• entire reset — deletes shadow branch + session state, would make it worse
• entire doctor — fixes stuck sessions, not the shadow branch lifecycle

Even a "one commit per prompt" workflow doesn't reliably work — Prompt 3's single commit (482a585) also failed to get linked.

Expected behavior

Every commit made during an active session should receive the Entire-Checkpoint trailer, as documented. The shadow branch should either:

1. Not be deleted until the session ends (not after each commit), or
2. Be recreated before returning from the post-commit hook, so it's available for the next commit's prepare-commit-msg, or
3. prepare-commit-msg should not depend on the shadow branch existing to decide whether to add the trailer — it should be sufficient that an active session exists for the worktree.

Steps to reproduce

1. entire configure --agent claude-code in any repo
2. Start a Claude Code session
3. Make 3+ commits in the same session (either in one turn or across turns)
4. Only the first commit gets the Entire-Checkpoint trailer
5. Dashboard shows subsequent commits without the Claude Code badge

entire.log

entire.tar.gz

Start with the post-commit hook and entire hooks git prepare-commit-msg, using .entire/logs/entire.log to trace shadow-branch deletion and trailer generation. Reproduce with multiple commits in one active session and verify that each commit receives an Entire-Checkpoint trailer without errors being silently swallowed.