fix: surface silent failures and drop unused dead-code paths (#193)

Address overengineering audit findings across cli/context/connector packages:

- F1 Snowflake `query`: drop bare catch that flattened all errors to empty result
- F2 memory-agent: treat LLM `stopReason === 'error'` as crash (skip squash-merge)
- F3 WikiSearchTool: description honest about token-only fallback vs sqlite-fts5 hybrid
- F5 Scan enrichment provider resolution: return discriminated status and surface
  distinct `llm_unavailable` / `embedding_unavailable` warnings per failure mode
- F6 Relationship validation budget: drop dead `tableCount === undefined → 'all'`
  branch; update tests to pass `tableCount` like production
- F8 `ktx sql`: use canonical `resolveOutputMode` (now honors KTX_OUTPUT/CI/TTY)
- F9 MCP stdio server: default `protocolIo.stderr` to `process.stderr` so
  memory_ingest startup failures are visible
- F13/F14 Scan/setup JSON readers: distinguish ENOENT from corruption instead of
  silently treating both as missing
- F15 `createKtxCliScanConnector`: throw config-shape error when driver matches
  but type guard rejects, instead of "no native connector"
- F16 ContextEvidenceSearchTool: surface `embedding_unhealthy:<reason>` instead
  of silently dropping the semantic lane
- F17 PromptService: default partials to `[]` (removes stale `clinical_policy`
  reference from a prior product)
- F20 `contextBuildCommands`: drop unused `runId` parameter

Dead-code removal:

- F4 Delete `AgentRunnerService` (duplicated `RuntimeAgentRunner`, only test-used);
  migrate tests to exercise `AiSdkKtxLlmRuntime.runAgentLoop` directly
- F7 Delete `KtxScanOrchestrator` and its test (no production callers; the
  inline pipeline in `runLocalScan` is the single source of truth)
- F18 Delete `generateKtxText`/`generateKtxObject` pass-through helpers; inline
  the single `runtime.generateObject` call at its caller

Plus a clarifying comment on the SQLite `resolveStringReference` `file:` carve-out
(load-bearing for SQLite URI form, not a bug).

packages/cli/src/setup-context.test.ts

@@ -206,7 +206,7 @@ describe('setup context build state', () => {
       reportIds: [],
       artifactPaths: [],
       retryableFailedTargets: [],
-      commands: contextBuildCommands(tempDir, 'setup-context-local-abc123'),
+      commands: contextBuildCommands(tempDir),
       failureReason: 'Previous foreground context build did not finish. Rerun setup or ktx ingest.',
       sourceProgress: [
         {
@@ -638,7 +638,7 @@ describe('setup context build state', () => {
       reportIds: [],
       artifactPaths: [],
       retryableFailedTargets: [],
-      commands: contextBuildCommands(tempDir, 'setup-context-local-stale'),
+      commands: contextBuildCommands(tempDir),
       failureReason: 'Previous foreground context build did not finish. Rerun setup or ktx ingest.',
     });
     const io = makeIo();