fix(core): skip nested repositories in snapshots

[opencode-agent]

Summary

• exclude directory-shaped untracked entries from snapshot staging
• keep ordinary untracked files in snapshot trees
• cover an unborn nested Git repository with a regression test

Why

Git reports embedded repositories as directory entries such as tui/. Passing one with no checked-out commit to the snapshot repository's git add fails the entire capture. With --untracked-files=all, ordinary directories are already expanded to their files, so directory entries can be omitted without losing normal file changes.

Testing

• bun test test/git.test.ts
• bun typecheck
• bun x prettier --check src/git.ts test/git.test.ts

Requested by: @rekram1-node (Aiden via Slack)

[Enough1122]

AI code review — automated review for reference, author can ignore or act on any point.

Sound fix. In packages/core/src/git.ts (hunk @@ -397,7, changed line 400), filtering directory-shaped entries out of candidates before staging prevents one unborn embedded repo (tui/) from failing the whole git add batch and stalling tree capture. Since the candidate list comes from NUL-separated git output, there is no path-quoting ambiguity, and a trailing slash cannot be part of a valid file name, so the filter cannot discard legitimate entries from either the tracked or untracked half. With --untracked-files=all, ordinary directories are already expanded, so nothing else is lost.

Suggestions:

1. The dropped entries now vanish silently. Consider logging the count/names of filtered directory entries so users can explain why a nested repo's files are absent from snapshots instead of filing "missing changes" bugs.
2. In packages/core/test/git.test.ts (new test, roughly lines 134–161), a companion case with a committed nested repo would document current behavior (git add records it as a gitlink) and guard the invariant if staging logic evolves.
3. Worth confirming no sibling code path builds staging candidates without this filter, so all snapshot entry points behave identically.