chore(workspace): gate dead-code with knip production mode (#196)

* refactor(workspace): relocate @ktx/llm source into packages/cli/src/llm

* refactor(workspace): rewrite @ktx/llm imports to relative paths

* refactor(workspace): fold internal packages into cli

* chore(workspace): gate dead-code with knip production mode

Turn on production-mode knip plus an autofix run in pre-commit and the
`pnpm dead-code` script, document the `/** @internal */` convention for
test-only exports in AGENTS.md, annotate test-only exports across the
CLI with that JSDoc, and drop dead exports/wrappers the new gate
surfaced (e.g. `cli-project.ts`, `lookerRuntimeSourceToFileAdapterSource`,
`createLocalScanEnrichmentProvidersFromConfig`,
`PGLITE_OWNER_PROCESS_BACKEND_CAPABILITIES`, stale type re-exports).
Replace the loose `ignoreIssues` allowlist in `knip.json` with explicit
production entries so cross-package barrel leaks are caught.

* 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.

* refactor(workspace): rename @ktx/cli to @kaelio/ktx and pack it directly

Promote the CLI workspace package to the public name `@kaelio/ktx` and
drop the separate `scripts/build-public-npm-package.mjs` wrapper. The
CLI package is now publishable in place (`publishConfig.access: public`,
`provenance: true`), so artifact packing uses `pnpm pack` against
`packages/cli/` instead of assembling a parallel package tree.

Updates all workspace filter invocations, docs, tests, and release
readiness checks to reference the new package name, and folds the
tarball-name helper into `scripts/public-npm-release-metadata.mjs`.

* docs: align "agent clients" and "data agents" terminology

Replace "client agents" with "agent clients" and "database agents" with
"data agents" across AGENTS.md, README.md, the docs-site copy, and the
matching setup-agents test description, matching the canonical
vocabulary in docs/terminology.md.

Also moves packages/cli/tsconfig.json's tsBuildInfoFile from
node_modules/.cache/ to dist/.tsbuildinfo so incremental builds survive
node_modules reinstalls.

* refactor(release): single source of truth for package version

Make packages/cli/package.json the single source of truth for the
@kaelio/ktx version. publicNpmPackageVersion() now reads it directly,
so artifact filenames, release-readiness checks, and the Python wheel
version all derive from one field. The duplicate
release-policy.json.publicNpmPackageVersion is removed.

Previously the two fields could drift: tarballs were named
kaelio-ktx-0.4.1.tgz while internally containing
@kaelio/ktx@0.0.0-private.

- update-public-release-version.mjs rewrites both Python pyproject.toml
  files (ktx-daemon, ktx-sl) alongside the npm package.jsons,
  normalizing the version for PEP 440 (e.g. 0.1.0-rc.2 -> 0.1.0rc2).
- semantic-release-config.cjs adds the two pyproject.toml files to
  @semantic-release/git assets so the release commit back to main
  carries every version source in lockstep.
- The six "?? '0.0.0-private'" fallback literals across the CLI are
  replaced with "?? getKtxCliPackageInfo().version", and
  createDefaultKtxMcpServer makes its version arg required.
- docs/release.md describes the actual commit-back model: the dev tree
  always reflects the most recent release; no sentinel pin to
  maintain.

Verified: pnpm run artifacts:build now produces
kaelio-ktx-0.4.1.tgz and kaelio_ktx-0.4.1-py3-none-any.whl with
@kaelio/ktx@0.4.1 inside. Full type-check, dead-code, and
2287 vitests + 173 script tests pass.

* refactor(cli): inject embedding provider resolution and detect sentence-transformers runtime

Make resolveProjectEmbeddingProvider and runtimeIo injectable in ingest and
scan command entrypoints so tests can stub them, and teach
resolvePublicIngestRuntimeRequirements to flag the local-embeddings runtime
feature when ktx.yaml selects sentence-transformers.

* chore(cli): mark buildLocalStatsStatus and LocalStatsStatus as @internal

Both symbols are consumed only by status-project.test.ts. Annotating with
/** @internal */ keeps knip's production-mode check clean without changing
runtime behavior.

* fix(cli): use real package metadata in print-command-tree

The stubbed package name embedded a forbidden product identifier that
tripped the boundary check in CI. Read the metadata from package.json
instead — keeps the rendered tree unchanged and removes a duplicate
source of truth.

* feat(cli): show embedding coverage in `ktx status`, drop duplicate disk counts

Inline `(N embedded)` next to the Wiki scope counts and Semantic-layer
source counts, computed with `SUM(embedding_json IS NOT NULL)` over
`knowledge_pages` and `local_sl_sources`. Rename the "Knowledge" label to
"Wiki" (canonical per `docs/terminology.md`) and rename the matching
`localStats.knowledgePages` field to `localStats.wikiPages`.

Drop `wiki=N md` and `semantic-layer=N yaml` from the Disk row — those
duplicated the per-surface rows above. Disk now reports only actual byte
usage (db, cache, raw-sources). The unused `wikiGlobalMarkdownCount` /
`semanticLayerYamlCount` fields, the `isMarkdownEntry` / `isYamlEntry`
helpers, and the `filter` arg on `summarizeDir` are removed.

packages/cli/src/context/project/project.ts

@@ -0,0 +1,146 @@
+import { promises as fs } from 'node:fs';
+import { basename, dirname, join, resolve } from 'node:path';
+import { GitService } from '../../context/core/git.service.js';
+import { type KtxCoreConfig, type KtxLogger, noopLogger } from '../../context/core/config.js';
+import type { KtxProjectConfig } from './config.js';
+import { buildDefaultKtxProjectConfig, parseKtxProjectConfig, serializeKtxProjectConfig } from './config.js';
+import { LocalGitFileStore } from './local-git-file-store.js';
+
+export interface InitKtxProjectOptions {
+  projectDir: string;
+  force?: boolean;
+  authorName?: string;
+  authorEmail?: string;
+  logger?: KtxLogger;
+}
+
+export interface LoadKtxProjectOptions {
+  projectDir: string;
+  authorName?: string;
+  authorEmail?: string;
+  logger?: KtxLogger;
+}
+
+export interface KtxLocalProject {
+  projectDir: string;
+  configPath: string;
+  config: KtxProjectConfig;
+  coreConfig: KtxCoreConfig;
+  git: GitService;
+  fileStore: LocalGitFileStore;
+}
+
+export interface InitKtxProjectResult extends KtxLocalProject {
+  commitHash: string | null;
+}
+
+const TRACKED_SCAFFOLD_FILES: Array<{ path: string; content: string }> = [
+  {
+    path: '.ktx/.gitignore',
+    content: 'cache/\ndb.sqlite\ndb.sqlite-*\ningest-transcripts/\nsecrets/\nsetup/\nagents/\n',
+  },
+  { path: '.ktx/prompts/.gitkeep', content: '' },
+  { path: '.ktx/skills/.gitkeep', content: '' },
+  { path: 'wiki/global/.gitkeep', content: '' },
+  { path: 'semantic-layer/.gitkeep', content: '' },
+  { path: 'raw-sources/.gitkeep', content: '' },
+];
+
+function createCoreConfig(projectDir: string, authorName: string, authorEmail: string): KtxCoreConfig {
+  return {
+    storage: {
+      configDir: projectDir,
+      homeDir: dirname(projectDir),
+      worktreesDir: join(projectDir, '.ktx/worktrees'),
+    },
+    git: {
+      userName: authorName,
+      userEmail: authorEmail,
+      bootstrapMessage: 'Initialize ktx project repository',
+      bootstrapAuthor: authorName,
+      bootstrapAuthorEmail: authorEmail,
+    },
+  };
+}
+
+async function fileExists(path: string): Promise<boolean> {
+  try {
+    await fs.access(path);
+    return true;
+  } catch {
+    return false;
+  }
+}
+
+async function writeProjectFile(projectDir: string, relativePath: string, content: string): Promise<void> {
+  const absolutePath = join(projectDir, relativePath);
+  await fs.mkdir(dirname(absolutePath), { recursive: true });
+  await fs.writeFile(absolutePath, content, 'utf-8');
+}
+
+async function createRuntime(
+  projectDir: string,
+  config: KtxProjectConfig,
+  authorName: string,
+  authorEmail: string,
+  logger: KtxLogger,
+): Promise<KtxLocalProject> {
+  const coreConfig = createCoreConfig(projectDir, authorName, authorEmail);
+  const git = new GitService(coreConfig, logger);
+  await git.onModuleInit();
+
+  return {
+    projectDir,
+    configPath: join(projectDir, 'ktx.yaml'),
+    config,
+    coreConfig,
+    git,
+    fileStore: new LocalGitFileStore({ rootDir: projectDir, git }),
+  };
+}
+
+export async function initKtxProject(options: InitKtxProjectOptions): Promise<InitKtxProjectResult> {
+  const projectDir = resolve(options.projectDir);
+  const projectName = basename(projectDir) || 'ktx-project';
+  const authorName = options.authorName ?? 'ktx';
+  const authorEmail = options.authorEmail ?? 'ktx@example.com';
+  const logger = options.logger ?? noopLogger;
+  const configPath = join(projectDir, 'ktx.yaml');
+
+  await fs.mkdir(projectDir, { recursive: true });
+  if (!options.force && (await fileExists(configPath))) {
+    throw new Error(`Project already contains ktx.yaml: ${configPath}`);
+  }
+
+  const config = buildDefaultKtxProjectConfig();
+  const runtime = await createRuntime(projectDir, config, authorName, authorEmail, logger);
+
+  await writeProjectFile(projectDir, 'ktx.yaml', serializeKtxProjectConfig(config));
+  await fs.mkdir(join(projectDir, '.ktx/cache'), { recursive: true });
+  for (const file of TRACKED_SCAFFOLD_FILES) {
+    await writeProjectFile(projectDir, file.path, file.content);
+  }
+
+  const commit = await runtime.git.commitFiles(
+    ['ktx.yaml', ...TRACKED_SCAFFOLD_FILES.map((file) => file.path)],
+    `Initialize KTX project: ${projectName}`,
+    authorName,
+    authorEmail,
+  );
+
+  return {
+    ...runtime,
+    commitHash: commit.commitHash,
+  };
+}
+
+export async function loadKtxProject(options: LoadKtxProjectOptions): Promise<KtxLocalProject> {
+  const projectDir = resolve(options.projectDir);
+  const authorName = options.authorName ?? 'ktx';
+  const authorEmail = options.authorEmail ?? 'ktx@example.com';
+  const logger = options.logger ?? noopLogger;
+  const configPath = join(projectDir, 'ktx.yaml');
+  const raw = await fs.readFile(configPath, 'utf-8');
+  const config = parseKtxProjectConfig(raw);
+  return createRuntime(projectDir, config, authorName, authorEmail, logger);
+}