refactor(cli): delete internal barrel index.ts files

The 34 `index.ts` re-export barrels inside `packages/cli/src/` were
holdovers from the pre-fold multi-workspace structure. Post-fold-in they
served no production purpose: external consumers go through the single
package main entry, and in-repo callers mostly imported through them
only because the path was short. Internally, knip flagged most barrel
re-exports as production-dead (only reached via tests).

This change:
- Deletes every internal barrel except `packages/cli/src/index.ts`
  (the published package entry).
- Rewrites ~270 source/test files to import each name directly from
  the file that defines it.
- Moves `tools/warehouse-verification/index.ts` to
  `create-warehouse-verification-tools.ts` (the function it defined
  locally) and updates its single consumer.
- Renames `search/backend-conformance.ts` → `.test-utils.ts` to match
  the existing test-helper file convention.
- Deletes 13 dead test-only chains (dbt-descriptions/*,
  live-database/extracted-schema, live-database/structural-sync,
  relationship-* feedback/review chain) plus their tests and a
  cascading orphan integration test.
- Updates test mocks that pointed at deleted barrel paths
  (notion-client, connector barrels in scan/local-scan-connectors
  tests) to mock the source files instead.
- Points the maintainer benchmark script
  (`scripts/relationship-benchmark-report.mjs`) at source files
  instead of `dist/context/scan/index.js`.
- Drops the barrel `!` entries from `knip.json`; adds explicit
  production entries only for the benchmark code reached via dist by
  the maintainer script.

Net: 413 files changed, ~1.2k insertions, ~9.4k deletions.

`pnpm run dead-code` (Biome + knip default + knip production) and
`pnpm run type-check` are clean; 2277 tests pass.

packages/cli/src/setup-sources.ts

@@ -2,32 +2,20 @@ import { mkdtemp, readdir, readFile, writeFile } from 'node:fs/promises';
 import { tmpdir } from 'node:os';
 import { join, relative, resolve } from 'node:path';
 import { fileURLToPath, pathToFileURL } from 'node:url';
-import {
-  localConnectionTypeForConfig,
-  resolveNotionConnectionAuthToken,
-} from './context/connections/index.js';
-import { resolveKtxConfigReference } from './context/core/index.js';
-import {
-  cloneOrPull,
-  DEFAULT_METABASE_CLIENT_CONFIG,
-  discoverMetabaseDatabases,
-  type DiscoveredMetabaseDatabase,
-  loadDbtSchemaFiles,
-  loadProjectInfo,
-  MetabaseClient,
-  type NotionApi,
-  NotionClient,
-  parseLookmlStagedDir,
-  parseMetricflowFiles,
-  testRepoConnection,
-} from './context/ingest/index.js';
-import {
-  type KtxProjectConfig,
-  type KtxProjectConnectionConfig,
-  loadKtxProject,
-  markKtxSetupStateStepComplete,
-  serializeKtxProjectConfig,
-} from './context/project/index.js';
+import { localConnectionTypeForConfig } from './context/connections/local-warehouse-descriptor.js';
+import { resolveNotionConnectionAuthToken } from './context/connections/notion-config.js';
+import { resolveKtxConfigReference } from './context/core/config-reference.js';
+import { cloneOrPull, testRepoConnection } from './context/ingest/repo-fetch.js';
+import { DEFAULT_METABASE_CLIENT_CONFIG, MetabaseClient } from './context/ingest/adapters/metabase/client.js';
+import { discoverMetabaseDatabases, type DiscoveredMetabaseDatabase } from './context/ingest/adapters/metabase/mapping.js';
+import { loadDbtSchemaFiles } from './context/ingest/dbt-shared/schema-files.js';
+import { loadProjectInfo } from './context/ingest/dbt-shared/project-vars.js';
+import { type NotionApi, NotionClient } from './context/ingest/adapters/notion/notion-client.js';
+import { parseLookmlStagedDir } from './context/ingest/adapters/lookml/parse.js';
+import { parseMetricflowFiles } from './context/ingest/adapters/metricflow/deep-parse.js';
+import { type KtxProjectConfig, type KtxProjectConnectionConfig, serializeKtxProjectConfig } from './context/project/config.js';
+import { loadKtxProject } from './context/project/project.js';
+import { markKtxSetupStateStepComplete } from './context/project/setup-config.js';
 import type { KtxCliIo } from './cli-runtime.js';
 import { pickNotionRootPages } from './notion-page-picker.js';
 import { runKtxSourceMapping } from './source-mapping.js';