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.ts

@@ -125,7 +125,7 @@ async function pathExists(path: string): Promise<boolean> {
   }
 }
 
-export function contextBuildCommands(projectDir: string, runId?: string): KtxSetupContextCommands {
+export function contextBuildCommands(projectDir: string): KtxSetupContextCommands {
   const resolvedProjectDir = resolve(projectDir);
   return {
     build: `ktx setup --project-dir ${resolvedProjectDir}`,
@@ -177,7 +177,7 @@ function normalizeState(projectDir: string, value: unknown): KtxSetupContextStat
     retryableFailedTargets: Array.isArray(record.retryableFailedTargets)
       ? record.retryableFailedTargets.filter((item): item is string => typeof item === 'string')
       : [],
-    commands: contextBuildCommands(projectDir, runId),
+    commands: contextBuildCommands(projectDir),
     ...(typeof record.failureReason === 'string' ? { failureReason: record.failureReason } : {}),
     ...(normalizeSourceProgress(record.sourceProgress) ? { sourceProgress: normalizeSourceProgress(record.sourceProgress) } : {}),
   };
@@ -241,7 +241,7 @@ export async function writeKtxSetupContextState(projectDir: string, state: KtxSe
   await mkdir(join(resolvedProjectDir, '.ktx', 'setup'), { recursive: true });
   const normalized = normalizeState(resolvedProjectDir, {
     ...state,
-    commands: contextBuildCommands(resolvedProjectDir, state.runId),
+    commands: contextBuildCommands(resolvedProjectDir),
   });
   await writeFile(statePath(resolvedProjectDir), `${JSON.stringify(normalized, null, 2)}\n`, 'utf-8');
 }
@@ -323,8 +323,11 @@ function stringArrayValue(value: unknown): string[] {
 async function readJsonFile(path: string): Promise<unknown | null> {
   try {
     return JSON.parse(await readFile(path, 'utf-8')) as unknown;
-  } catch {
-    return null;
+  } catch (error) {
+    if (error instanceof Error && (error as NodeJS.ErrnoException).code === 'ENOENT') {
+      return null;
+    }
+    throw new Error(`Failed to read JSON file ${path}: ${error instanceof Error ? error.message : String(error)}`);
   }
 }
 
@@ -549,7 +552,7 @@ async function runBuild(
     reportIds: [],
     artifactPaths: [],
     retryableFailedTargets: [],
-    commands: contextBuildCommands(args.projectDir, runId),
+    commands: contextBuildCommands(args.projectDir),
     failureReason: 'Previous foreground context build did not finish. Rerun setup or ktx ingest.',
   };
   await writeKtxSetupContextState(args.projectDir, incompleteState);
@@ -663,7 +666,7 @@ async function completeExistingContext(
     reportIds: [],
     artifactPaths: [],
     retryableFailedTargets: [],
-    commands: contextBuildCommands(args.projectDir, runId),
+    commands: contextBuildCommands(args.projectDir),
   });
   writeExistingContextSuccess(readiness, io);
   return { status: 'ready', projectDir: args.projectDir, runId };