Rewording commits can silently break Entire linkage when Entire-Checkpoint trailers are dropped

[SvenMeyer]

Summary

Rewording existing commits (for example via git rebase -i/reword or git filter-branch --msg-filter) can silently break Entire session linkage if the rewrite replaces the full commit message and drops the Entire-Checkpoint: trailer.

I hit this in a repo using Entire + Factory AI Droid. After renaming three commit subjects, those three commits lost their [Factory AI Droid] label and session link in the Entire UI, while two adjacent rewritten commits remained linked.

Environment

• Entire CLI: 0.5.2 (5affe173)
• OS: Linux (Manjaro)
• Agent: Factory AI Droid
• Git remote: GitHub

What I observed

We intended to rename only 3 of the last 5 commits.

The history-rewrite command rewrote the full 5-commit range, so all 5 commits got new hashes. However, 2 of those commits kept their exact original message and Entire-Checkpoint: trailer and remained correctly linked in Entire, while the 3 commits whose message text was replaced lost their trailer and therefore lost the Entire/agent label in the UI.

The resulting rewritten 5-commit segment looked like this:

old commit	old subject	new commit	new subject	trailer after rewrite?	Entire label in UI?
211e583	feat: complete retirement flow with ProjectStore records	5ce6a31	feat: task-060.3-implement-retirement-metadata-split	no	no
a340deb	chore: add combined quiet validator gate	96155f5	chore: add combined quiet validator gate	yes	yes
c68b67b	chore: streamline validator output	837f1fc	chore: streamline validator output	yes	yes
39f8ad0	feat: store project verification records in ProjectStore	dd24525	feat: task-060.2-implement-verification-records-in-project-store	no	no
ae92a5c	refactor: centralize issuance records in ProjectStore	ec034b9	refactor: task-060.1-migrate-issuance-records-into-project-store	no	no

The difference was not code content or author identity. The difference was that the three renamed commits had their full message replaced, so their Entire-Checkpoint: trailer disappeared.

Evidence from git

Before rewrite, the affected commits had trailers:

211e583
feat: complete retirement flow with ProjectStore records

Entire-Checkpoint: 85eda2fe566e

39f8ad0
feat: store project verification records in ProjectStore

Entire-Checkpoint: c63eb21633ef

ae92a5c
refactor: centralize issuance records in ProjectStore

Entire-Checkpoint: a4c7fecd47a5

After rewrite, the renamed commits no longer had trailers:

5ce6a31
feat: task-060.3-implement-retirement-metadata-split

dd24525
feat: task-060.2-implement-verification-records-in-project-store

ec034b9
refactor: task-060.1-migrate-issuance-records-into-project-store

But the rewritten commits whose messages were preserved still retained their trailers:

96155f5
chore: add combined quiet validator gate

Entire-Checkpoint: 0e30151eed18

837f1fc
chore: streamline validator output

Entire-Checkpoint: e19149854b98

Also, the repo still has Entire session refs keyed to the original commit prefixes, e.g.:

refs/heads/entire/a340deb-e3b0c4
refs/heads/entire/39f8ad0-e3b0c4
refs/heads/entire/ae92a5c-e3b0c4

Why I think this is worth fixing/documenting

I understand that a rewritten commit gets a new SHA, so simple SHA tracking alone cannot survive rewording.

But from a user perspective this is still pretty surprising:

• the commit still represents the same logical work/session
• Entire metadata clearly existed before the rewrite
• a normal history-cleanup operation can silently orphan the session link if the trailer line is lost
• there is no obvious warning or repair flow

Expected behavior

Any of these would help:

1. Document this limitation clearly: if users reword or rewrite commits, they must preserve Entire-Checkpoint: trailers manually.
2. Warn or auto-preserve: provide guidance when Entire detects a rewritten commit flow that removed a known trailer.
3. Repair tooling: add a command to relink/reimport checkpoints after a history rewrite.
4. More robust linkage: if possible, use additional metadata so commit rewording is not so easy to orphan.

Minimal reproduction

1. Create a commit during an active Entire-linked agent session so the commit gets an Entire-Checkpoint: trailer.
2. Rewrite that commit message with a method that replaces the full message body, e.g.:
   • git rebase -i + manual edit that removes trailers, or
   • git filter-branch --msg-filter that outputs only a new one-line subject.
3. Force-push the rewritten branch.
4. Observe that the rewritten commit no longer shows the Entire agent/session label in the UI.

If useful, I can provide a more exact command transcript from this repo.

[peyton-alt]

Thanks for filing this, we've seen it and it's on our radar. We'll update this issue as we investigate. If you have additional logs, please add them here.