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>

client.py

@@ -9,11 +9,15 @@ import json
 import os
 from pathlib import Path
 
+from dotenv import load_dotenv
 from claude_code_sdk import ClaudeCodeOptions, ClaudeSDKClient
 from claude_code_sdk.types import HookMatcher
 
 from security import bash_security_hook
 
+# Load environment variables from .env file
+load_dotenv()
+
 
 # Puppeteer MCP tools for browser automation
 PUPPETEER_TOOLS = [
@@ -85,15 +89,17 @@ def create_client(project_dir: Path, model: str) -> ClaudeSDKClient:
     api_key = os.environ.get("CLAUDE_CODE_OAUTH_TOKEN")
     if not api_key:
         raise ValueError(
-            "CLAUDE_CODE_OAUTH_TOKEN environment variable not set.\n"
-            "Run 'claude setup-token after installing the Claude Code CLI."
+            "CLAUDE_CODE_OAUTH_TOKEN not set in .env file.\n"
+            "Run 'claude setup-token' after installing the Claude Code CLI,\n"
+            "then add the token to your .env file."
         )
 
     linear_api_key = os.environ.get("LINEAR_API_KEY")
     if not linear_api_key:
         raise ValueError(
-            "LINEAR_API_KEY environment variable not set.\n"
-            "Get your API key from: https://linear.app/YOUR-TEAM/settings/api"
+            "LINEAR_API_KEY not set in .env file.\n"
+            "Get your API key from: https://linear.app/YOUR-TEAM/settings/api\n"
+            "then add it to your .env file."
         )
 
     # Create comprehensive security settings