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/services/assistant_chat_session.py

@@ -76,7 +76,8 @@ def get_system_prompt(project_name: str, project_dir: Path) -> str:
     """Generate the system prompt for the assistant with project context."""
     # Try to load app_spec.txt for context
     app_spec_content = ""
-    app_spec_path = project_dir / "prompts" / "app_spec.txt"
+    from autocoder_paths import get_prompts_dir
+    app_spec_path = get_prompts_dir(project_dir) / "app_spec.txt"
     if app_spec_path.exists():
         try:
             app_spec_content = app_spec_path.read_text(encoding="utf-8")
@@ -235,7 +236,9 @@ class AssistantChatSession:
                 "allow": permissions_list,
             },
         }
-        settings_file = self.project_dir / ".claude_assistant_settings.json"
+        from autocoder_paths import get_claude_assistant_settings_path
+        settings_file = get_claude_assistant_settings_path(self.project_dir)
+        settings_file.parent.mkdir(parents=True, exist_ok=True)
         with open(settings_file, "w") as f:
             json.dump(security_settings, f, indent=2)