fix: read semantic sources safely (#284)

* fix: read semantic sources safely

* test: retarget reindex per-scope error case to a broken manifest

Reading a broken standalone source was made non-fatal in de1f1a8d (it is
surfaced for repair instead of throwing), so the reindex per-scope error
test no longer captured an error. Point it at a corrupt manifest shard,
which is the remaining fatal read failure the per-scope catch must
isolate, and assert the captured error names the offending file.

* fix(sl): decouple semantic-layer file names from warehouse naming rules

The in-file `name:` field is now the sole source identity; the filename is
a derived label that never participates in identity. This removes the
"Unsafe semantic-layer source name" failure class entirely: any warehouse
identifier (Snowflake's uppercase SIGNED_UP, EVENT$LOG, dotted names) can
be read, overlaid, edited, and deleted.

- New `source-files.ts`: one total filename derivation (safe lowercase
  names verbatim; otherwise slug + sha256-hash suffix, immune to
  case-insensitive-filesystem collisions) and one by-name file resolver.
- Reads resolve by name everywhere; the path-from-name fast path and
  `assertSafeSourceName` are gone.
- Writes resolve-then-write: rewrites land on the file that declares the
  name (human renames survive); new sources get a derived filename; a
  derived path occupied by a different source fails instead of clobbering.
- `readSourceFile` returns null for missing files instead of forcing every
  caller to launder IO errors; `deleteSource` distinguishes manifest-backed
  sources from not-found instead of silently succeeding.
- `sl_write_source` accepts verbatim warehouse identifiers (snake_case is
  now a recommendation for new sources) and rejects sourceName/source.name
  mismatches; `sl_edit_source` rejects name-changing edits.
- Ingest projection commits, gate-repair allowlists, and touched-source
  derivation use resolved paths / in-file names instead of interpolating
  `<connId>/<name>.yaml`.
- Collapsed the five parallel path derivations and duplicated path-token
  helpers onto the shared module; dropped dead service methods.

* fix(sl): resolve sources by declared name end-to-end and gate warehouse SQL with the parser-backed validator

- Key broken/renamed semantic-layer files by their recoverable in-file
  name (slSourceNameForFile) so mid-edit sources stay reachable under
  their real identity in reads, listings, and search
- Derive finalization touched sources from composed-source diffs and
  recover deleted files' declared names from the pre-change commit
  instead of parsing hash-derived filenames
- Resolve revert/rollback paths against history (listFilesAtCommit) so
  human-renamed files are restored where they lived at preHead
- Validate ingest sql_execution through the daemon's sqlglot
  validateReadOnly in the connection's dialect, sharing one
  driver-to-dialect map (sql-analysis/dialect.ts) across MCP and ingest
- Harden the local read-only SQL backstop: accept leading comments,
  reject smuggled second statements, and strip trailing
  semicolons/comments before row-limit wrapping

packages/cli/test/context/core/git.service.test.ts

@@ -1,6 +1,6 @@
-import { mkdtemp, readFile, realpath, rm, writeFile } from 'node:fs/promises';
+import { mkdir, mkdtemp, readFile, realpath, rm, writeFile } from 'node:fs/promises';
 import { tmpdir } from 'node:os';
-import { join } from 'node:path';
+import { dirname, join } from 'node:path';
 import { afterEach, beforeEach, describe, expect, it } from 'vitest';
 import type { KtxCoreConfig } from '../../../src/context/core/config.js';
 import { GitService } from '../../../src/context/core/git.service.js';
@@ -35,10 +35,29 @@ describe('GitService', () => {
   });
 
   const writeAndCommit = async (filePath: string, content: string, message = 'msg') => {
+    await mkdir(dirname(join(tempDir, filePath)), { recursive: true });
     await writeFile(join(tempDir, filePath), content, 'utf-8');
     return service.commitFile(filePath, message, 'Test', 'test@example.com');
   };
 
+  describe('listFilesAtCommit', () => {
+    it('lists matching paths at a commit and recovers files deleted since', async () => {
+      await writeAndCommit('semantic-layer/warehouse/custom.yaml', 'name: orders\n');
+      const atSeed = await service.revParseHead();
+      await service.deleteFile('semantic-layer/warehouse/custom.yaml', 'drop', 'Test', 'test@example.com');
+
+      // HEAD no longer has the file; the seed commit still does.
+      await expect(service.listFilesAtCommit('semantic-layer/warehouse', 'HEAD')).resolves.toEqual([]);
+      await expect(service.listFilesAtCommit('semantic-layer/warehouse', atSeed)).resolves.toEqual([
+        'semantic-layer/warehouse/custom.yaml',
+      ]);
+    });
+
+    it('returns [] for a pathspec that matches nothing', async () => {
+      await expect(service.listFilesAtCommit('does/not/exist', 'HEAD')).resolves.toEqual([]);
+    });
+  });
+
   describe('cold-start bootstrap commit', () => {
     it('writes an empty commit on init so HEAD always resolves', async () => {
       // beforeEach already ran onModuleInit() against an empty temp dir.