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/index-sync/reindex.test.ts

@@ -159,13 +159,16 @@ describe('reindexLocalIndexes', () => {
       '---\nsummary: Revenue\nusage_mode: auto\n---\n\nPaid orders.\n',
       'utf-8',
     );
-    await mkdir(join(project.projectDir, 'semantic-layer/warehouse'), { recursive: true });
-    await writeFile(join(project.projectDir, 'semantic-layer/warehouse/broken.yaml'), 'not: [valid', 'utf-8');
+    // A broken standalone source is surfaced for repair rather than failing the
+    // scope, so use a corrupt machine-generated manifest shard, which is the
+    // remaining fatal read failure that the per-scope catch must isolate.
+    await mkdir(join(project.projectDir, 'semantic-layer/warehouse/_schema'), { recursive: true });
+    await writeFile(join(project.projectDir, 'semantic-layer/warehouse/_schema/broken.yaml'), 'not: [valid', 'utf-8');
 
     const summary = await reindexLocalIndexes(project, { force: false, embeddingService: null });
 
     expect(summary.scopes.find((scope) => scope.label === 'global')?.error).toBeUndefined();
-    expect(summary.scopes.find((scope) => scope.label === 'warehouse')?.error).toContain('YAML');
+    expect(summary.scopes.find((scope) => scope.label === 'warehouse')?.error).toContain('_schema/broken.yaml');
   });
 
   it('marks a scope errored when configured embeddings fail', async () => {