v3.4.40 — Naming at scale: classifier fix, hygiene trash scan, root MANIFEST, hot-path perf

[3.4.40] — 2026-07-27

Patch release: the naming-at-scale wave — slug/theme quality, hot-path performance, store self-description, and the hygiene "trash scan".

Fixed

• Theme/sig classifier over-matching: autoClassifyTheme/autoClassifySig matched vocabulary, not conditions — \bmcp\b treated the hyphen in "novada-mcp" as a word boundary, so any summary mentioning that project name classified as mcp-unavailable (measured: 29/32 = 90.6% of one project's journal filenames). Classifiers now require co-occurring condition signals in the same clause; misclassification drops to 1/31 with the survivor genuine. Two shadow epidemics (version-bump, agent-fix) that would have surfaced behind the first fix are fixed in the same pass. Enums unchanged — old filenames parse forever.
• alignment KPI staleness: the session_start scan-dedup initially threaded a pre-write snapshot into getCorrectionKPIs, making alignment null exactly when a never-retrieved P0 was first surfaced. The KPI call site reads fresh after this call's own retrieved-outcome writes (caught by independent integration review, pinned as a regression test).

Added

• ar hygiene — the trash scan: 8 detection-only store checks (junk/test project dirs, ambient-counter accumulation, theme epidemics, case-fold fork dirs, stale derived caches, root-level credential patterns, missing corrections/_index.md, reserved-word slugs) with a baseline so repeat runs report only NEW findings. Detection-only by contract: it never deletes, renames, or quarantines; every finding carries an agent_instruction; secret findings report pattern name + line number, never the matched text. Fresh RED findings → exit 1 (cron-friendly). Not part of the MCP tool surface.
• Store-root MANIFEST.md (write-once, generated beside the per-project MEMORY-PROTOCOL.md): makes a bare store directory self-describing for any agent with filesystem access — cold-agent read order, sync / never-sync / regenerable file classification (config.json explicitly marked never-sync, do-not-read), and a condensed naming-grammar cheat-sheet. All paths store-root-relative; the MEMORY-PROTOCOL.md template's hardcoded ~ path is now root-relative too.

Performance

• session_start corrections scans: 4 → 2. One shared snapshot feeds P0 surfacing, prediction, and recognition; the KPI computation deliberately re-reads after this call's own outcome writes (see Fixed). At the measured 50k-file extreme this cuts ~2s from every session_start.
• Legacy journal index (index.md/index.jsonl) is incremental: only files with mtime newer than the index are re-read; unchanged rows merge from the previous index.jsonl by filename. It previously re-read every journal body TWICE per journal_write/rollup/merge/archive (2.8s at 50k files; now pays only for what changed). Kept rather than removed because a live MCP resource (agent-recall://{project}/index) reads it verbatim.