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Colby MchenryandClaude Opus 5.5
1cb4aab913
When the indexed project is a folder of its git repository (a monorepo package, an app/ folder beside a server/ one), `codegraph status`, `status --json` and the freshness check behind codegraph_status reported the index up to date while `codegraph sync` found the very same changes. `git status --porcelain` prints paths from the repository root whatever folder it runs in, and reports the whole repository. Change detection joined `app/src/index.js` under the project, found nothing at `app/app/src/index.js`, and dropped it. The dirty paths a sync records for the restore check (from PR #1878) were stored the same way, so a file put back with git after a sync was missed too. And a project in a folder its repository gitignores got a permanently clean answer from git, which says nothing about an ignored folder. Change detection now asks where the project sits in its repository (`git rev-parse --show-prefix`, kept per folder, and skipped when the folder has its own .git). Below the root it runs git status with a `-- .` pathspec, takes the prefix off every path and leaves out anything outside the folder. The project's ignore rules match those project-relative paths, the recorded dirty paths are project-relative, and a project its repository ignores declines the git path as the scan already did, so callers take the full scan. A project at its repository root runs exactly the git command it ran before. Validation: - git-status-subdir-project.test.ts (new, 7 cases): edited, added and deleted files in a subdir project, matching sync; edits outside the project left out, with the pathspec asserted; the restore case, across a reopen; the project's own anchored .gitignore rule; an embedded repo inside the project; the gitignored-project fallback; and a repo-root project running exactly today's status command with no prefix call. 6 fail on main's source; the repo-root control passes on both. Four mutations (no pathspec, ignore rules on repo-relative paths, no fallback, no .git shortcut) each fail the test. - CLI repros: after an edit and an added file in app/, status --json reads 0/0/0 on main and 1 added + 1 modified with the fix; the same in a gitignored project; a subdir restore reads 0 on main and 1 modified with the fix (a repo-root project reads 1 on both). - The MCP freshness worker on a subdir project: 0/0/0 on main, 1 added + 1 modified with the fix. Reported in PR #1636 by @innoxxicide. This reimplements the fix independently, on top of the restore check that landed after it. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>