Files
cubelinux-2/cubesys
CUBELinux-2 bd3e3c0512 cubesys/notes: note tag <coord> <cat> (in-place recategorize); close out the notes -> model CUBE integration + error-tracing from prior run data saved in CUBE
note tag
- New `cube note tag <coord> <cat>` subcommand: reclassify an existing note in place by
  setting its doc_type to `note:<cat>` and put_record under the same coord. Used to move
  mis-tagged notes into the right category (e.g. a finding accidentally logged as a debug
  or action). Puts are WAL+delta+checkpoint durable. Note: `delete_raw` is NOT durable here
  (the checkpoint/delta records Puts of surviving keys only — no tombstones — so a deleted
  key resurrects from the base snapshot on reload), so `tag` is the reliable in-place
  reclassify path. 5 notes tests pass.

Notes -> model CUBE integration (message-save-path)
- cubesys:🎶 WordFlags-tagged CZYX note log (doc_type=note:<category>); project threads
  via linked_records; project resume (<cubecoords> project resume <name> <text>) and context
  injection (<project context <name>>). Durable ConcurrentStore (WAL + delta + checkpoint);
  short-lived processes must checkpoint() before exit.
- CLI: cube note add|list|search|show; cube project list|show|resume|context.
- cube-notes-mcp (stdio MCP server) exposes mcp__cubenotes__note_*/project_* tools to the
  DeepSeek Harness; harness registers the mcp-client at the BUNDLE layer (inject: [tools])
  so the plugin actually mounts (profile-layer rows can't inject the tools service — the
  silent no-mount bug).

How we used it: trace errors from prior run data saved in CUBE
- The headless agent (cube-agent) treats CUBE as a searchable, replayable log: every action
  is written as a note (category=action) so a run can be replayed/fine-tuned; each review run
  reads ONLY uncovered findings (category=finding) and marks them covered with a checkpoint
  note (category=checkpoint) — true incremental, non-destructive review.
- The deterministic, grounded report tool reads finding notes verbatim (no model
  hallucination), assigns severity (HIGH/MEDIUM/LOW) + priority order, and writes a review
  .txt. It surfaced 7 previously un-categorized logs (GIT-SHALLOW-CLONE, POSTFIX-TLS-CERTS,
  SELINUX-RESTORECON, DSH-WEB-EADDRINUSE, CONCURRENT-STORE-CHECKPOINT, MCP-BUNDLE-LAYER,
  CUBES-TWO-TREES) that were logged but never tagged finding.
- Coverage is precise: the report marks exactly the findings it reviewed, so the next run
  reports only new ones. The notes store is also the harness GUI's CUBE surface
  (mcp-cubenotes note_list), so everything the agent writes is visible and reviewable.
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