docs: record the mail fixes and the collection rename

Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>

TODO.md

@@ -43,26 +43,27 @@ and green (674 tests, three consecutive clean runs).
       per request. Needs an admin setting for which collections to search, then
       fan-out and merge — `dedupeSources` in `src/utils/clinicalRetrieval.js`
       already merges and renumbers. See `clinical-assist/COLLECTIONS.md`.
-- [ ] **Confirm mail indexing end to end.** Six separate breaks are fixed, and
+- [x] **Mail indexing works.** It was never reached: mail ran last, after nine
-      mail is enabled (`BASIC_INDEXING_MAIL_ENABLED=true`), but no mail has been
+      other sources, and Tables alone is thousands of rows at about a second
-      indexed yet: the file pass was still working through 472 large PDFs (68
+      each. Mail leads now — it is the only bounded source (identities only,
-      done in six hours, some over 1,500 chunks each) and mail runs after it.
+      capped by `BASIC_INDEXING_MAIL_MAX_MESSAGES`, bodies left to the
-      On 2026-09-11 the indexed folder was changed from `Documents` to
+      processor), so it cannot starve the others the way they starved it.
-      `Personal assistant`, which currently lists 0 files, so the file pass is
+      Messages are indexing.
-      now trivial and mail should be reached on a scan cycle (every 300s).
+- [x] **Mail attachments were never indexed.** An attachment's id is its index
-      Watch for `[SCAN-*] Mail messages: N seen, M queued`.
+      within its message, so `/api/attachments/{id}` meant nothing and answered
-      Note: the 68 files already indexed from `Documents` are still in the
+      500 every time. Fixed to `/api/messages/{id}/attachment/{id}`, verified
-      collection. Say the word if they should be cleared.
+      live against a real message.
-- [ ] **`image-size` DoS advisory (high), no upstream fix.** Every published
+- [x] **The basic collection is renamed** `personal_assistant_bge_m3_1024`
-      version up to 2.0.2 is affected; `npm audit fix` only offers a breaking
+      (was `basic_bge_m3_1024_v2`), matching `mcp_bge_m3_1024` on the clinical
-      downgrade of pptxgenjs. Not reachable here: the only `addImage` call
+      side. Milvus grants name the collection, so the rename revoked
-      (`src/routes/learningAI.js`) is fed PNGs the app generated itself and
+      basic_reader/basic_writer; `bootstrap_basic.py` restored them, but it
-      fetched with an ownership check, never an uploaded file. Uploads are
+      must be bind-mounted because the operator image ships an older copy.
-      allowlisted to jpeg/png/gif and checked against their magic bytes. Revisit
+- [ ] **The indexed folder is `Personal assistant`,** and the setting now takes
-      when pptxgenjs ships a patched dependency.
+      a comma-separated list (`Personal assistant,Clinical Notes`), each walked
-- [ ] **`uuid` advisory (moderate) via gaxios via Google auth.** Not reachable:
+      recursively. Note the file reconciliation removed the chunks of the 68
-      the flaw needs v3/v5/v6 with an explicit buffer, and gaxios calls only
+      `Documents` files, since a complete listing is the deletion authority and
-      `v4()` for a multipart boundary. Forcing an override risks Vertex auth.
+      they are no longer under an indexed root. Entities went 27,930 -> ~9,700.
+      Re-add those files under an indexed folder if they are still wanted.
 
 ## Deployment readiness (CI/CD and Kubernetes)