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>

.claude/settings.local.json

@@ -3,7 +3,41 @@
     "allow": [
       "Bash(test:*)",
       "Bash(cat:*)",
-      "Bash(netstat:*)"
+      "Bash(netstat:*)",
+      "Bash(docker-compose:*)",
+      "Bash(ls:*)",
+      "Bash(rm:*)",
+      "Bash(python autonomous_agent_demo.py:*)",
+      "Bash(dir C:GitHublinear_coding_philosophia_raggenerationslibrary_rag*.py)",
+      "Bash(git add:*)",
+      "Bash(git commit -m \"$\\(cat <<''EOF''\nFix import error: rename delete_document_passages to delete_document_chunks\n\nThe function was renamed in weaviate_ingest.py but the import in __init__.py\nwas not updated, causing ImportError when using the library.\n\nChanges:\n- Updated import statement in utils/__init__.py\n- Updated __all__ export list to use correct function name\nEOF\n\\)\")",
+      "Bash(dir \"C:\\\\GitHub\\\\linear_coding_philosophia_rag\\\\generations\\\\library_rag\\\\.env\")",
+      "Bash(git commit:*)",
+      "Bash(tasklist:*)",
+      "Bash(findstr:*)",
+      "Bash(wmic process:*)",
+      "Bash(powershell -Command \"Get-Process python | Select-Object Id,Path,StartTime | Format-Table -AutoSize\")",
+      "Bash(powershell -Command \"Get-WmiObject Win32_Process -Filter \"\"name = ''python.exe''\"\" | Select-Object ProcessId, CommandLine | Format-List\")",
+      "Bash(timeout:*)",
+      "Bash(powershell -Command:*)",
+      "Bash(python:*)",
+      "Bash(dir \"C:\\\\GitHub\\\\linear_coding_library_rag\\\\generations\\\\library_rag\")",
+      "Bash(docker ps:*)",
+      "Bash(curl:*)",
+      "Bash(dir:*)",
+      "Bash(grep:*)",
+      "Bash(git push:*)",
+      "Bash(mypy:*)",
+      "WebSearch",
+      "Bash(nvidia-smi:*)",
+      "WebFetch(domain:cr.weaviate.io)",
+      "Bash(git restore:*)",
+      "Bash(git log:*)",
+      "Bash(done)",
+      "Bash(git remote set-url:*)",
+      "Bash(docker compose:*)",
+      "Bash(pytest:*)",
+      "Bash(git pull:*)"
     ]
   }
 }