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170eefd4a0
`gitnexus status` reported "stale (re-run gitnexus analyze)" whenever the working tree held any modified or untracked file, including files the index never reads. Because `analyze` cannot commit, stash or delete such a file, the remedy it prescribed could not clear the verdict — the only way back to up-to-date was to remove the file. `meta.fileHashes` already records the exact set of files a run covered, so answer the question directly: compare those hashes against disk, reusing analyze's own scan, hash and diff helpers so the two cannot disagree about what "changed" means. A new coverable file still counts as stale (the index is genuinely incomplete then), but one `analyze` now settles it. The repo-wide dirty flag survives only as the fallback for metadata written before `fileHashes` existed. Both freshness checks now read GitNexus's own analyze output (AGENTS.md, CLAUDE.md, the agent skill mirrors) from one shared list. They previously held separate copies, and since analyze rewrites those files after recording hashes, a per-file comparison that missed them would report a freshly indexed repository as permanently stale. Closes #3077 Co-authored-by: Gergo Magyar <gergomagyar0@gmail.com> Co-authored-by: Cursor <cursoragent@cursor.com> |
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