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>

linear_config.py

@@ -7,10 +7,14 @@ These values are used in prompts and for project state management.
 """
 
 import os
+from dotenv import load_dotenv
 
-# Environment variables (must be set before running)
+# Load environment variables from .env file
+load_dotenv()
+
+# Environment variables (loaded from .env file)
 LINEAR_API_KEY = os.environ.get("LINEAR_API_KEY")
-LINEAR_TEAM_ID  = os.environ.get("LINEAR_TEAM_ID") 
+LINEAR_TEAM_ID = os.environ.get("LINEAR_TEAM_ID") 
 
 # Default number of issues to create (can be overridden via command line)
 DEFAULT_ISSUE_COUNT = 50