Update framework configuration and clean up obsolete specs

Configuration updates:
- Added .env.example template for environment variables
- Updated README.md with better setup instructions (.env usage)
- Enhanced .claude/settings.local.json with additional Bash permissions
- Added .claude/CLAUDE.md framework documentation

Spec cleanup:
- Removed obsolete spec files (language_selection, mistral_extensible, template, theme_customization)
- Consolidated app_spec.txt (Claude Clone example)
- Added app_spec_model.txt as reference template
- Added app_spec_library_rag_types_docs.txt
- Added coding_prompt_library.md

Framework improvements:
- Updated agent.py, autonomous_agent_demo.py, client.py with minor fixes
- Enhanced dockerize_my_project.py
- Updated prompts (initializer, initializer_bis) with better guidance
- Added docker-compose.my_project.yml example

This commit consolidates improvements made during development sessions.

🤖 Generated with [Claude Code](https://claude.com/claude-code)

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

autonomous_agent_demo.py

@@ -17,8 +17,12 @@ import asyncio
 import os
 from pathlib import Path
 
+from dotenv import load_dotenv
 from agent import run_autonomous_agent
 
+# Load environment variables from .env file
+load_dotenv()
+
 
 # Configuration
 # Using Claude Opus 4.5 as default for best coding and agentic performance
@@ -48,9 +52,10 @@ Examples:
   # Add new specifications to existing project
   python autonomous_agent_demo.py --project-dir ./claude_clone --new-spec app_spec_new1.txt
 
-Environment Variables:
+Configuration (.env file):
   CLAUDE_CODE_OAUTH_TOKEN    Claude Code OAuth token (required)
   LINEAR_API_KEY             Linear API key (required)
+  LINEAR_TEAM_ID             Linear Team ID (optional)
         """,
     )
 
@@ -91,18 +96,17 @@ def main() -> None:
 
     # Check for Claude Code OAuth token
     if not os.environ.get("CLAUDE_CODE_OAUTH_TOKEN"):
-        print("Error: CLAUDE_CODE_OAUTH_TOKEN environment variable not set")
-        print("\nRun 'claude setup-token' after installing the Claude Code CLI.")
-        print("\nThen set it:")
-        print("  export CLAUDE_CODE_OAUTH_TOKEN='your-token-here'")
+        print("Error: CLAUDE_CODE_OAUTH_TOKEN not found in .env file")
+        print("\n1. Run 'claude setup-token' after installing the Claude Code CLI")
+        print("2. Copy .env.example to .env")
+        print("3. Add your token to .env: CLAUDE_CODE_OAUTH_TOKEN='your-token-here'")
         return
 
     # Check for Linear API key
     if not os.environ.get("LINEAR_API_KEY"):
-        print("Error: LINEAR_API_KEY environment variable not set")
-        print("\nGet your API key from: https://linear.app/YOUR-TEAM/settings/api")
-        print("\nThen set it:")
-        print("  export LINEAR_API_KEY='lin_api_xxxxxxxxxxxxx'")
+        print("Error: LINEAR_API_KEY not found in .env file")
+        print("\n1. Get your API key from: https://linear.app/YOUR-TEAM/settings/api")
+        print("2. Add it to .env: LINEAR_API_KEY='lin_api_xxxxxxxxxxxxx'")
         return
 
     # Automatically place projects in generations/ directory unless already specified