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>

.claude/skills/gsd-to-autocoder-spec/SKILL.md

@@ -9,7 +9,7 @@ description: |
 
 # GSD to Autocoder Spec Converter
 
-Converts `.planning/codebase/*.md` (GSD mapping output) to `prompts/app_spec.txt` (Autocoder format).
+Converts `.planning/codebase/*.md` (GSD mapping output) to `.autocoder/prompts/app_spec.txt` (Autocoder format).
 
 ## When to Use
 
@@ -84,7 +84,7 @@ Extract:
 
 Create `prompts/` directory:
 ```bash
-mkdir -p prompts
+mkdir -p .autocoder/prompts
 ```
 
 **Mapping GSD Documents to Autocoder Spec:**
@@ -114,7 +114,7 @@ mkdir -p prompts
 **Write the spec file** using the XML format from [references/app-spec-format.md](references/app-spec-format.md):
 
 ```bash
-cat > prompts/app_spec.txt << 'EOF'
+cat > .autocoder/prompts/app_spec.txt << 'EOF'
 <project_specification>
   <project_name>{from package.json or directory}</project_name>
 
@@ -173,9 +173,9 @@ EOF
 ### Step 5: Verify Generated Spec
 
 ```bash
-head -100 prompts/app_spec.txt
+head -100 .autocoder/prompts/app_spec.txt
 echo "---"
-grep -c "User can\|System\|API\|Feature" prompts/app_spec.txt || echo "0"
+grep -c "User can\|System\|API\|Feature" .autocoder/prompts/app_spec.txt || echo "0"
 ```
 
 **Validation checklist:**
@@ -194,7 +194,7 @@ Output:
 app_spec.txt generated from GSD codebase mapping.
 
 Source: .planning/codebase/*.md
-Output: prompts/app_spec.txt
+Output: .autocoder/prompts/app_spec.txt
 
 Next: Start Autocoder