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/commands/create-spec.md

@@ -8,7 +8,7 @@ This command **requires** the project directory as an argument via `$ARGUMENTS`.
 
 **Example:** `/create-spec generations/my-app`
 
-**Output location:** `$ARGUMENTS/prompts/app_spec.txt` and `$ARGUMENTS/prompts/initializer_prompt.md`
+**Output location:** `$ARGUMENTS/.autocoder/prompts/app_spec.txt` and `$ARGUMENTS/.autocoder/prompts/initializer_prompt.md`
 
 If `$ARGUMENTS` is empty, inform the user they must provide a project path and exit.
 
@@ -347,13 +347,13 @@ First ask in conversation if they want to make changes.
 
 ## Output Directory
 
-The output directory is: `$ARGUMENTS/prompts/`
+The output directory is: `$ARGUMENTS/.autocoder/prompts/`
 
 Once the user approves, generate these files:
 
 ## 1. Generate `app_spec.txt`
 
-**Output path:** `$ARGUMENTS/prompts/app_spec.txt`
+**Output path:** `$ARGUMENTS/.autocoder/prompts/app_spec.txt`
 
 Create a new file using this XML structure:
 
@@ -489,7 +489,7 @@ Create a new file using this XML structure:
 
 ## 2. Update `initializer_prompt.md`
 
-**Output path:** `$ARGUMENTS/prompts/initializer_prompt.md`
+**Output path:** `$ARGUMENTS/.autocoder/prompts/initializer_prompt.md`
 
 If the output directory has an existing `initializer_prompt.md`, read it and update the feature count.
 If not, copy from `.claude/templates/initializer_prompt.template.md` first, then update.
@@ -512,7 +512,7 @@ After:  **CRITICAL:** You must create exactly **25** features using the `feature
 
 ## 3. Write Status File (REQUIRED - Do This Last)
 
-**Output path:** `$ARGUMENTS/prompts/.spec_status.json`
+**Output path:** `$ARGUMENTS/.autocoder/prompts/.spec_status.json`
 
 **CRITICAL:** After you have completed ALL requested file changes, write this status file to signal completion to the UI. This is required for the "Continue to Project" button to appear.
 
@@ -524,8 +524,8 @@ Write this JSON file:
   "version": 1,
   "timestamp": "[current ISO 8601 timestamp, e.g., 2025-01-15T14:30:00.000Z]",
   "files_written": [
-    "prompts/app_spec.txt",
-    "prompts/initializer_prompt.md"
+    ".autocoder/prompts/app_spec.txt",
+    ".autocoder/prompts/initializer_prompt.md"
   ],
   "feature_count": [the feature count from Phase 4L]
 }
@@ -539,9 +539,9 @@ Write this JSON file:
   "version": 1,
   "timestamp": "2025-01-15T14:30:00.000Z",
   "files_written": [
-    "prompts/app_spec.txt",
-    "prompts/initializer_prompt.md",
-    "prompts/coding_prompt.md"
+    ".autocoder/prompts/app_spec.txt",
+    ".autocoder/prompts/initializer_prompt.md",
+    ".autocoder/prompts/coding_prompt.md"
   ],
   "feature_count": 35
 }
@@ -559,11 +559,11 @@ Write this JSON file:
 
 Once files are generated, tell the user what to do next:
 
-> "Your specification files have been created in `$ARGUMENTS/prompts/`!
+> "Your specification files have been created in `$ARGUMENTS/.autocoder/prompts/`!
 >
 > **Files created:**
-> - `$ARGUMENTS/prompts/app_spec.txt`
-> - `$ARGUMENTS/prompts/initializer_prompt.md`
+> - `$ARGUMENTS/.autocoder/prompts/app_spec.txt`
+> - `$ARGUMENTS/.autocoder/prompts/initializer_prompt.md`
 >
 > The **Continue to Project** button should now appear. Click it to start the autonomous coding agent!
 >

.claude/commands/expand-project.md

@@ -42,7 +42,7 @@ You are the **Project Expansion Assistant** - an expert at understanding existin
 # FIRST: Read and Understand Existing Project
 
 **Step 1:** Read the existing specification:
-- Read `$ARGUMENTS/prompts/app_spec.txt`
+- Read `$ARGUMENTS/.autocoder/prompts/app_spec.txt`
 
 **Step 2:** Present a summary to the user:
 
@@ -231,4 +231,4 @@ If they want to add more, go back to Phase 1.
 
 # BEGIN
 
-Start by reading the app specification file at `$ARGUMENTS/prompts/app_spec.txt`, then greet the user with a summary of their existing project and ask what they want to add.
+Start by reading the app specification file at `$ARGUMENTS/.autocoder/prompts/app_spec.txt`, then greet the user with a summary of their existing project and ask what they want to add.

.claude/commands/gsd-to-autocoder-spec.md

@@ -5,6 +5,6 @@ description: Convert GSD codebase mapping to Autocoder app_spec.txt
 
 # GSD to Autocoder Spec
 
-Convert `.planning/codebase/*.md` (from `/gsd:map-codebase`) to Autocoder's `prompts/app_spec.txt`.
+Convert `.planning/codebase/*.md` (from `/gsd:map-codebase`) to Autocoder's `.autocoder/prompts/app_spec.txt`.
 
 @.claude/skills/gsd-to-autocoder-spec/SKILL.md

.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