fix(types): add TypeScript declarations for JS modules with gitignore exception

Add comprehensive .d.ts files for all JS modules imported by TypeScript source.
Update .gitignore to allow src/resources/extensions/**/*.d.ts (hand-written
declarations for JS modules) while keeping src/**/*.d.ts ignored for compiled output.

- preferences: 16 exported functions
- preferences-models: 20 exported functions including isProviderModelAllowed
- gitignore: 6 exported functions
- agentic-docs-scaffold: SCAFFOLD_FILES + ensureAgenticDocsScaffold
- doc-checker: DocCheckResult interface with summary stub/missing counts
- code-intelligence: 21 exports including backend constants, optional prefs param
- native-git-bridge: 50+ git operations
- paths: 30+ path resolution functions
- repo-identity: 9 exported functions
- trace-collector: Span/Trace interfaces + 12 functions
- types: SFState interface with activeMilestone/phase/nextAction
- doctor: 5 exported functions including runSFDoctor
- url-utils: 8 exported functions
- config: RemoteConfig interface + 4 functions

.gitignore

@@ -8,6 +8,8 @@ src/**/*.js.map
 src/**/*.d.ts
 src/**/*.d.ts.map
 !src/**/*.test.js
+# Allow hand-written .d.ts for JS modules consumed by TypeScript
+!src/resources/extensions/**/*.d.ts
 
 # ── Repowise index (local machine-generated cache) ──
 .repowise/