memora 0.3.2

Consolidated 0.3.x release. Notes for the earlier 0.3.x tags remain in the repo as
RELEASE_NOTES_0.3.0.md and RELEASE_NOTES_0.3.1.md.

Fresh installs work again

mcp 2.0.0 removed mcp.server.fastmcp, and our dependency was an unbounded mcp>=1.0.0, so every
fresh install resolved to the new major and the server died at import with
ModuleNotFoundError. Now constrained to mcp>=1.0.0,<2 (the 1.x line is maintained in parallel).

The failure was invisible from both sides: a dead stdio MCP server looks identical to one exposing no
tools, and existing environments had mcp pinned to a working 1.x, so every test suite passed.

Reported and fixed by @BillyBunn in
#44.

Breaking

Embeddings. memora could be configured — following its own installer and README — into a state
where no embedding was ever computed and nothing said so. install.sh generated
openai/text-embedding-3-small while the README recommended OpenRouter as the base URL, and
OpenRouter serves no embeddings endpoint. Every call 404'd, one warning went to a log nobody reads,
and stores silently filled with TF-IDF keyword bags. In the store where this was found, 756 memories
had been keyword vectors for months.

• Every store needs one embedding rebuild. The model fingerprint now records backend, model,
  endpoint host and representation, so the old bare "openai" stamp no longer matches.
• Dense backends no longer fall back to TF-IDF. A provider failure raises instead of persisting a
  wrong vector. Set tfidf explicitly if you want it.
• MEMORA_EMBEDDING_API_KEY / MEMORA_EMBEDDING_BASE_URL are an atomic pair — set both or
  neither. A partial pair is rejected rather than borrowing the missing half from OPENAI_*, which
  could previously send one provider's secret to another provider's host.

Issues are no longer inferred. memory_create_issue and memory_create_todo are now the only
ways a memory becomes typed; memory_absorb and plain creates stay untyped knowledge. A keyword
classifier had mislabelled 130 knowledge memories as open issues. Existing typed memories are
untouched.

Added

• memory_verify_integrity — read-only doctor reporting representation counts, coverage and
  offending ids, with concrete remediation.
• MEMORA_EMBEDDING_STRICT=1 (recommended) turns a broken endpoint into a named error instead of
  silent degradation.
• Integrity derived from SQL and invalidated by a DB-owned change epoch, so an external writer cannot
  leave a stale "healthy" verdict behind.

Fixed

• Batch embedding responses are validated for cardinality, index coverage and uniform dimensions, and
  reconstructed by index — a reordered response could previously attach a vector to the wrong
  memory.
• Coverage uses indexed anti-joins in both directions; counting by subtraction let one orphan cancel
  one missing embedding.
• absorb no longer leaves untracked partial rows.
• Concurrent ensure_schema no longer raises on duplicate columns.
• install.sh and the README no longer generate or document the broken configuration.

memora-graph

• Supersession is visible. Superseded memories render dimmed amber with a SUPERSEDED badge and
  directed lineage arrows; a toggle collapses to current-state only. Only supersedes edges count as
  lineage — references/contradicts/implements were previously drawn as supersession. Half-written
  crossrefs are detected rather than shown as current, and the page reports
  LINEAGE UNAVAILABLE instead of a confident zero when it cannot tell.
• The 3D view no longer burns the CPU. Its render loop repainted 60×/sec forever, whether or not
  anything changed — measured at ~227% CPU on an idle page. The loop now stops once the layout
  settles and wakes on interaction: ~227% → 0.4%. Kill switch:
  localStorage.setItem("memora-graph.noIdle","1").
• Resizable timeline and detail drawers with independently persisted widths; per-tab panel widths in
  the default view.
• The database selector lists every configured database in both views (it was hardcoded in one).
• The top bar no longer hides behind open drawers.

Known issues

• Epoch time-of-check window — a query can use data that changed mid-call; the next call detects
  it. Transient, self-healing.
• memories_embedding_repairs is unbounded with no foreign key to memory lifetime; explicit id
  reuse can mark an unrelated row as recurring.
• D1 ownership recovery after a lost response lacks bounded retry and a unique operation record.
• External writers must populate the new columns. A writer emitting a thresholded/sparse encoding
  of a dense vector is reported as an encoding fault by id, and auto-rebuild is skipped deliberately.
• The default index.html view lacks force-graph's database-switch protection — after a switch or
  live refresh an already-rendered list can briefly show another store's authority state. Memory ids
  overlap across databases, so this is worth knowing.

Upgrading

1. Upgrade, then run memory_verify_integrity before anything else.
2. If it reports a repairable mismatch, run an embedding rebuild.
3. Set MEMORA_EMBEDDING_STRICT=1.
4. Verify by looking at a stored vector, not at your config — it should have your model's
   dimension count with numeric keys covering 0..N-1. Configuration that looks correct is what hid
   the original problem.