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/sql.ts

@@ -2,13 +2,14 @@ import { loadKtxProject, type KtxLocalProject } from '@ktx/context/project';
 import type { KtxQueryResult, KtxScanConnector } from '@ktx/context/scan';
 import type { SqlAnalysisDialect, SqlAnalysisPort } from '@ktx/context/sql-analysis';
 import type { KtxCliIo } from './cli-runtime.js';
+import { type KtxOutputMode, resolveOutputMode } from './io/mode.js';
 import { createKtxCliScanConnector } from './local-scan-connectors.js';
 import { createManagedDaemonSqlAnalysisPort } from './managed-python-http.js';
 import { profileMark } from './startup-profile.js';
 
 profileMark('module:sql');
 
-type KtxSqlOutputMode = 'pretty' | 'plain' | 'json';
+type KtxSqlOutputMode = KtxOutputMode;
 
 export type KtxSqlArgs = {
   command: 'execute';
@@ -53,11 +54,6 @@ function sqlAnalysisDialectForDriver(driver: string | undefined): SqlAnalysisDia
   return map[normalized] ?? 'postgres';
 }
 
-function resolveOutputMode(args: KtxSqlArgs): KtxSqlOutputMode {
-  if (args.json === true) return 'json';
-  return args.output ?? 'pretty';
-}
-
 function formatValue(value: unknown): string {
   if (value === null || value === undefined) return '';
   if (typeof value === 'string') return value;
@@ -159,7 +155,8 @@ export async function runKtxSql(args: KtxSqlArgs, io: KtxCliIo = process, deps:
         },
         { runId: 'cli-sql' },
       );
-      printSqlResult(resultOutput(args.connectionId, result), resolveOutputMode(args), io);
+      const mode = resolveOutputMode({ explicit: args.output, json: args.json, io });
+      printSqlResult(resultOutput(args.connectionId, result), mode, io);
       return 0;
     } finally {
       await cleanupConnector(connector);