refactor: sqlc vs raw SQL — hybrid approach (R3)
Deleted 8 genuinely unused sqlc queries (no inline equivalent): - UpsertCurrentRelationship, ListEntitiesCapped, ListEntityStatus, UpdateSignalState, InsertClassification, InsertFeedback, InsertSkill, UpsertCurrentRelationship — all had zero call sites. Migrated 9 inline raw SQL sites to use sqlc queries: - GetOntology (impl.go): ListEntityTypes, ListRelationshipTypes, ListLifecycleDefs — replaces 3 raw pool.Query blocks with typed sqlcgen calls, eliminating manual row scanning. - EndRelationship (phase3.go): EndCurrentRelationship — replaces tx.Exec with sqlcgen.New(tx).EndCurrentRelationship. - checkPrecondition (impl.go): GetEntityStatus — replaces tx.QueryRow + manual Scan with sqlcgen.New(tx).GetEntityStatus. - GetEntityRelations (impl.go): ListEntityRelations — replaces raw pool.Query + scanRelationships helper (now deleted). - GetGraph (impl.go): ListGraphEdges — replaces raw pool.Query + scanRelationships. - resolveEntityID (impl.go): GetEntityBySlug/GetEntityByID — replaces raw pool.QueryRow + Scan. - createApproval (mcp/server.go): InsertApproval — replaces raw pool.Exec with sqlcgen.InsertApproval. Deleted scanRelationships helper (was only used by the two migrated graph queries above). Regenerated sqlcgen — also picks up stale model updates (AgentSession, SessionPlanStep, SessionQuestion, etc. from recent migrations). Documented the carve-out in .agents/dev/CONTRIBUTING.md §SQL conventions: sqlc is the default; raw pool.Query/Exec is reserved for LISTEN/NOTIFY, dynamic WHERE builders, blast_radius(), and COPY. go vet, build, httpapi/mcp/db tests all pass. -383/+170 lines.
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@@ -399,7 +399,7 @@ behavior; tracked as R6.
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| R1 | Delete dead Go: `notifier.VerifyApprovalToken`, `httpapi/stubs.go`; unexport 4 `checkdefaults` symbols | S | Low | ✅ done (c3973e7) |
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| R2 | Delete dead web: 21-file tool-renderer registry, 5 dead components, 2 dead store exports, 2 dead npm deps | S | Low | ✅ done (c3973e7+1) |
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| R3 | Decide sqlc vs raw SQL: delete 17 dead queries OR migrate inline SQL to use them | M | Medium |
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| R3 | Decide sqlc vs raw SQL: delete 17 dead queries OR migrate inline SQL to use them | M | Medium | ✅ done (hybrid: 8 deleted, 9 migrated) |
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| R4 | Split `phase3.go` (2627 lines) into per-resource files; refactor `newServer` (708 lines) to a tool registry | M | Medium |
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| R5 | Rewrite `.agents/domains/knowledge/schema.md` + `.agents/shared/llm-wiki.md` for the DB-native model; delete/deprecate root `inventory.yaml` | M | Low |
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| R6 | Inject desktop `version` from `VERSION` via ldflags; fix `Makefile` `BINARY` colliding with `oikos/` dir | S | Low |
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