First step for any issue: run longhand doctor. It reports database, hook, MCP, and index health in one shot.

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Run longhand reconcile to check for drift between ~/.claude/projects/ and the sessions table. Two common causes:

• SessionEnd hook didn't fire — the transcript is on disk but was never ingested (hook failure, Claude Code exit path that skipped hooks, transcript predates longhand hook install).
• Project inference attributed to $HOME — sessions launched from your home directory with $HOME as the first-event cwd got project_id = NULL on pre-0.6.0 ingest. Fixed at ingest time in v0.6.0 for new sessions.

Both are resolved by longhand reconcile --fix. The reconciler is idempotent — the already_ingested check plus upsert_session mean you can re-run safely.

As of v0.6.0, recall_project_status also surfaces a stale: true flag with a stale_reason string whenever it detects on-disk transcripts not ingested for the queried project. If an agent sees that flag and silently falls back to reading raw JSONLs, the recall skill is out of date — refresh ~/.claude/skills/recall/SKILL.md from the repo.

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Open an issue at github.com/Wynelson94/longhand/issues with the output of longhand doctor and whatever command you ran. Include your OS, Python version, and Claude Code version.