feat: move autocoder runtime files into .autocoder/ subdirectory

Add centralized path resolution module (autocoder_paths.py) that
consolidates all autocoder-generated file paths behind a dual-path
strategy: check .autocoder/X first, fall back to root-level X for
backward compatibility, default to .autocoder/X for new projects.

Key changes:
- New autocoder_paths.py with dual-path resolution for features.db,
  assistant.db, lock files, settings, prompts dir, and progress cache
- migrate_project_layout() safely moves old-layout projects to new
  layout with SQLite WAL flush and integrity verification
- Updated 22 files to delegate path construction to autocoder_paths
- Reset/delete logic cleans both old and new file locations
- Orphan lock cleanup checks both locations per project
- Migration called automatically at agent start in autonomous_agent_demo.py
- Updated markdown commands/skills to reference .autocoder/prompts/
- CLAUDE.md documentation updated with new project structure

Files at project root that remain unchanged:
- CLAUDE.md (Claude SDK reads from cwd via setting_sources=["project"])
- app_spec.txt root copy (agent templates reference it via cat)

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

server/routers/features.py

@@ -134,7 +134,8 @@ async def list_features(project_name: str):
     if not project_dir.exists():
         raise HTTPException(status_code=404, detail="Project directory not found")
 
-    db_file = project_dir / "features.db"
+    from autocoder_paths import get_features_db_path
+    db_file = get_features_db_path(project_dir)
     if not db_file.exists():
         return FeatureListResponse(pending=[], in_progress=[], done=[])
 
@@ -329,7 +330,8 @@ async def get_dependency_graph(project_name: str):
     if not project_dir.exists():
         raise HTTPException(status_code=404, detail="Project directory not found")
 
-    db_file = project_dir / "features.db"
+    from autocoder_paths import get_features_db_path
+    db_file = get_features_db_path(project_dir)
     if not db_file.exists():
         return DependencyGraphResponse(nodes=[], edges=[])
 
@@ -393,7 +395,8 @@ async def get_feature(project_name: str, feature_id: int):
     if not project_dir.exists():
         raise HTTPException(status_code=404, detail="Project directory not found")
 
-    db_file = project_dir / "features.db"
+    from autocoder_paths import get_features_db_path
+    db_file = get_features_db_path(project_dir)
     if not db_file.exists():
         raise HTTPException(status_code=404, detail="No features database found")