fix(agentdb): add delete API — closes #150 (ruflo#1784 / RuVector#427 chain)

[ruvnet]

Summary

Closes the agentdb-side gap from this chain:

• agentdb hierarchical-store and causal-edge have no delete tools — blocks full re-index of ADRs ruflo#1784 — agentdb_hierarchical-store / agentdb_causal-edge MCP tools have no delete tools, breaking /adr-index re-runs after ADR file deletion.
• @ruvector/graph-node binding has no delete API — blocks downstream re-indexing RuVector#427 — closed but the binding-level methods are still pending publish on @ruvector/graph-node@2.0.4.
• agentdb: GraphDatabaseAdapter has no delete methods — blocks downstream re-indexing (ruflo#1784, RuVector#427) #150 — this PR.

The native @ruvector/graph-node binding exposes only createNode / createEdge / createHyperedge / searchHyperedges as documented methods, but GraphDatabase.prototype.query(cypher) is also live. We implement delete by routing through Cypher so consumers get a delete API today without waiting for binding-level methods.

What ships

New on GraphDatabaseAdapter (packages/agentdb/src/backends/graph/GraphDatabaseAdapter.ts)

Method	Notes
deleteNode(id, { cascade?: boolean }): { deletedNode, deletedEdges }	Counts incident edges before delete so the count is accurate regardless of binding stats. cascade: false refuses with a typed error when edges exist (matches RuVector#427 spec).
deleteEdge(id): { deleted }	Endpoints stay intact.
deleteHyperedge(id): { deleted }	Match scoped with :HYPEREDGE to disambiguate from regular relationships.
deleteEdgesByEndpoints(from, to, label?): { deleted }	Saves callers from materialising every edge id when they want to scrub a (source, target, label) tuple.
escapeId / escapeLabel	Cypher-injection guards — labels validated against /^[A-Za-z_][A-Za-z0-9_]*$/ so 'evil; DROP' throws instead of slipping into the query.

New on ReflexionMemory

• deleteEpisode(id: number \| string): boolean — mirrors the dual-write pattern from reflexion.storeEpisode() does not INSERT into episodes/episode_embeddings SQL tables #128 in reverse. Routes through graph adapter / generic graph backend / vector backend (when present) AND always purges SQL episodes and episode_embeddings rows so durable storage stays in sync.

Tests

packages/agentdb/tests/unit/controllers/ReflexionMemory-delete.test.ts — 10 tests, all passing:

• 3 ReflexionMemory.deleteEpisode tests against an in-memory SQL fake
• 7 GraphDatabaseAdapter Cypher-emission tests against a CypherSpy that records every query() call:
  • DETACH DELETE wiring + accurate edge count
  • cascade: false refusal with edge count
  • edge-by-id
  • hyperedge :HYPEREDGE label scoping
  • endpoint-tuple delete
  • label injection guard
  • id escaping for embedded quotes/backslashes

cd packages/agentdb && npx vitest run tests/unit/controllers/ReflexionMemory-delete.test.ts
Test Files  1 passed (1)
     Tests  10 passed (10)

The existing 23-test verification suite for the prior issue fixes (#145, #146, #102, #110, #118/119, #128, #129) is also still passing — no regressions.

Why Cypher and not bind-level

The native binding doesn't expose deleteNode / deleteEdge / deleteHyperedge even on the latest published @ruvector/graph-node@2.0.4. RuVector#427 is closed but those methods aren't on the registry yet. Rather than block on republishing the binding, we route through Cypher (MATCH (n {id: $id}) DETACH DELETE n RETURN count(n)) — same end result, no upstream-publish dependency. When the binding ships native methods, this adapter can switch to those without breaking the public API.

Downstream

Once this is published as agentdb@3.0.0-alpha.13, ruvnet/ruflo#1789's stub branches at bridgeDeleteCausalNode / bridgeDeleteCausalEdge can re-target their primary path at graphAdapter.deleteNode / .deleteEdge. The SQL fallback then becomes a true fallback — only fires when the graph backend isn't loaded.

Closes #150

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