Add Library RAG project and cleanup root directory

- Add complete Library RAG application (Flask + MCP server)
  - PDF processing pipeline with OCR and LLM extraction
  - Weaviate vector database integration (BGE-M3 embeddings)
  - Flask web interface with search and document management
  - MCP server for Claude Desktop integration
  - Comprehensive test suite (134 tests)

- Clean up root directory
  - Remove obsolete documentation files
  - Remove backup and temporary files
  - Update autonomous agent configuration

- Update prompts
  - Enhance initializer bis prompt with better instructions

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

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

generations/library_rag/examples/KNOWN_ISSUES.md

@@ -0,0 +1,71 @@
+# Known Issues - MCP Client
+
+## 1. Author/Work Filters Not Supported (Weaviate Limitation)
+
+**Status:** Known limitation
+**Affects:** `search_chunks` and `search_summaries` tools
+**Error:** Results in server error when using `author_filter` or `work_filter` parameters
+
+**Root Cause:**
+Weaviate v4 does not support filtering on nested object properties. The `work` field in the Chunk schema is defined as:
+
+```python
+wvc.Property(
+    name="work",
+    data_type=wvc.DataType.OBJECT,
+    nested_properties=[
+        wvc.Property(name="title", data_type=wvc.DataType.TEXT),
+        wvc.Property(name="author", data_type=wvc.DataType.TEXT),
+    ],
+)
+```
+
+Attempts to filter on `work.author` or `work.title` result in:
+```
+data type "object" not supported in query
+```
+
+**Workaround:**
+
+Use the `filter_by_author` tool instead:
+
+```python
+# Instead of:
+search_chunks(
+    query="nominalism",
+    author_filter="Charles Sanders Peirce"  # ❌ Doesn't work
+)
+
+# Use:
+filter_by_author(
+    author="Charles Sanders Peirce"  # ✓ Works
+)
+```
+
+Or search without filters and filter client-side:
+
+```python
+results = await client.call_tool("search_chunks", {
+    "query": "nominalism",
+    "limit": 50  # Fetch more
+})
+
+# Filter in Python
+filtered = [
+    r for r in results["results"]
+    if r["work_author"] == "Charles Sanders Peirce"
+]
+```
+
+**Future Fix:**
+
+Option 1: Add flat properties `workAuthor` and `workTitle` to Chunk schema (requires migration)
+Option 2: Implement post-filtering in Python on the server side
+Option 3: Wait for Weaviate to support nested object filtering
+
+**Tests Affected:**
+
+- `test_mcp_client.py::test_search_chunks` - Works without filters
+- Search with `author_filter` - Currently fails
+
+**Last Updated:** 2025-12-25