fix(memory-store): supersession + per-fact provenance end-to-end

[Peefy]

Summary

The schema already supported soft-deprecation (deprecated_at, deprecation_reason, superseded_by_summary_id plus a partial WHERE deprecated_at IS NULL index), and deprecateMessages was implemented on RawMessageStorageManager, but the search layer, CLI, and synthesis prompt never saw them. A user repro (three versions of a decision, two deprecated) saw all three tie at similarity 1.000 and the lex tiebreaker picked arbitrarily; per-fact provenance (metadata.source) was visible in list --json but stripped from search --json and from the LLM synthesis context. There was also no CLI deprecate subcommand, so users had to drop into JS to deprecate anything.

Changes

• Plumb includeDeprecated end-to-end — adds the field to SearchInput / UnifiedMemorySearchInput, threads it through runSemanticSearchForEmbedding and runLexicalSearchForKeywords (both the dep functions and the SQLite fallbacks), and adds --include-deprecated to opencontext search (default off, preserves current-truth).
• New opencontext deprecate CLI subcommand — mirrors add's shape; flags --user (required), --id (repeatable, required), --reason, --superseded-by, --json, --help. Calls getRawMessageManager().deprecateMessages(...).
• Surface per-fact provenance — SearchEvidence.metadata now carries the underlying hit's metadata. CLI --context-only prints a source: <uri-or-em-dash> line per evidence item. buildSynthesisPrompt line format is now [n] (id, source=<uri-or-tier-or-'unknown'>, score=N.NNNN) snippet, with metadata.source taking precedence over the channel-level source.
• Fix vec0 KNN deprecation-blindness — wraps searchChunksWithVectorTable in a 3-attempt widen-and-retry loop (cap 4096 to respect sqlite-vec's k value in knn query too large limit) so limit is preserved even when most top-K candidates are deprecated. Adds a cross-reference comment on the parent-level mirror in searchMessagesWithVectorTable so the two vec0 KNN paths stay in sync.

Verification

User's repro (clean SQLite-backed memory store):

=== step 1: ingest three versions ===
REST    = 31acd868-b328-4169-818a-f822ccd92001
GraphQL = ad80216b-3af6-4494-a4de-35d889947dd9
tRPC    = 16ef97bd-0969-4f16-9b11-9d9ce1d6fa10

=== step 2: deprecate the older two via the new deprecate CLI ===
deprecated 1 message: 31acd868-...
deprecated 1 message: ad80216b-...

=== step 3: idempotency check (re-deprecate REST) ===
{"ok":true,"exit":0,"count":0,"ids":["31acd868-..."],"deprecatedAt":...}

=== step 4: top-1 current-truth (default hides deprecated) — expect tRPC only ===
  count = 1
  - memory:16ef97bd sim=1.0000 src=meeting://2026-08-15 | Public API: tRPC
  evidence[0].metadata.source = "meeting://2026-08-15"

=== step 5: --include-deprecated audit view — expect all 3 ===
  count = 3
  - memory:16ef97bd sim=1.0000 src=meeting://2026-08-15 | Public API: tRPC
  - memory:31acd868 sim=1.0000 src=meeting://2026-03-01 | Public API: REST
  - memory:ad80216b sim=1.0000 src=meeting://2026-06-01 | Public API: GraphQL

=== step 6: --context-only shows per-fact source ===
# user=u1 query="Public API"
# count=1 (no synthesis call made)
[1.000] raw @ 2026-08-15T00:00:00.000Z
    id: 16ef97bd-...
    source: meeting://2026-08-15
    Public API: tRPC

Test plan

• pnpm --filter @melandlabs/opencontext test — 109/109 pass (added 3 tests: default includeDeprecated is omitted, --include-deprecated forwards true, --context-only surfaces per-fact metadata.source)
• pnpm --filter @melandlabs/memory-store test — 203/203 search tests pass
• pnpm --filter @melandlabs/sqlite test — 23/23 pass
• pnpm --filter @melandlabs/indexeddb test — 10/10 pass
• User's repro: add × 3 → deprecate × 2 → search --limit 1 returns tRPC only; --include-deprecated returns all 3; idempotent re-deprecate reports count=0

The two pre-existing test failures on main (applicability-propagation.test.ts:292 readonly/mutable cast, and cli-shared.test.ts @melandlabs/rag/chroma-vector-store resolution) are unrelated to this change — both confirmed pre-existing via git stash round-trip.

🤖 Generated with Claude Code