Add a memories table (survives index rebuilds) for agent-written
conclusions with provenance (session, message range, project). The agent
writes markdown files via Write tool (user-approved), then registers
them via a --remember CodeAct script with remember(). Recall via
memories() in --query scripts, filtered by project/session/time.
Separates query (read-only, assertReadOnlySql) from remember (write)
execution contexts in runtime.mjs.
Split the monolithic skill prompt into three tiers:
- Core API (search/context/sql) stays in the first prompt
- Structured helpers listed as one-liners with filter signatures
- Detailed patterns and pitfalls extracted to references/
Add references/query-patterns.md (copyable CodeAct recipes) and
references/pitfalls.md (scope, FTS, ordering, compactness traps).
Clarify project scope semantics (slug vs path vs cwd) throughout.
Add ORDER BY timestamp DESC to failures() for newest-first default.
Previously the session metadata accumulator started from zero on every
reindex pass, so an incremental update would overwrite started_at and
message_count with values derived only from the new lines.
Now reads the existing session row first and merges new data on top.
tommy0103