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>

prompts/initializer_bis_prompt.md

@@ -60,6 +60,13 @@ using the `mcp__linear__create_issue` tool.
 - Do NOT modify existing issues
 - Only create NEW issues for the NEW features
 
+**IMPORTANT - Issue Count:**
+Create EXACTLY ONE issue per feature listed in the `<implementation_steps>` section of the new spec file.
+- If the spec has 8 features → create 8 issues
+- If the spec has 15 features → create 15 issues
+- Do NOT create a fixed number like 50 issues
+- Each `<feature_N>` in the spec = 1 Linear issue
+
 **For each NEW feature, create an issue with:**
 
 ```