Improve document processing pipeline and agent workflows

- Add delete_document_chunks for reprocessing, save extracted text to disk
- Expand case directory structure (original/extracted/proofread/backup)
- Update classifier patterns (תגובה, הודעת עמדה)
- Fix proofreader agent paths for new directory layout
- Update HEARTBEAT to notify on every task completion
- Improve bidi_table with LRE/PDF directional embedding
- Add Paperclip project verification and auto-close setup issue
- Add auto-sync-cases.sh for Gitea synchronization

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

mcp-server/src/legal_mcp/services/db.py

@@ -687,6 +687,16 @@ async def update_decision(decision_id: UUID, **fields) -> None:
 
 # ── Chunks & Vectors ───────────────────────────────────────────────
 
+async def delete_document_chunks(document_id: UUID) -> int:
+    """Delete all chunks for a document (used before reprocessing)."""
+    pool = await get_pool()
+    async with pool.acquire() as conn:
+        result = await conn.execute(
+            "DELETE FROM document_chunks WHERE document_id = $1", document_id
+        )
+        return int(result.split()[-1])  # e.g. "DELETE 5" -> 5
+
+
 async def store_chunks(
     document_id: UUID,
     case_id: UUID | None,

mcp-server/src/legal_mcp/services/local_classifier.py

@@ -19,7 +19,7 @@ logger = logging.getLogger(__name__)
 _FILENAME_RULES: list[tuple[str, str, float]] = [
     # (regex pattern on filename, doc_type, confidence)
     (r"כתב.ערר|כתב-ערר", "appeal", 1.0),
-    (r"תשובה|תשובת|תגובת|השלמת.טיעון|בקשה.להשלמת", "response", 1.0),
+    (r"תשובה|תשובת|תגובה|תגובת|השלמת.טיעון|בקשה.להשלמת|הודעת.עמדה", "response", 1.0),
     (r"פרוטוקול", "protocol", 1.0),
     (r"החלטת?.ביניים|החלטה.לתיקון", "decision", 0.95),
     (r"הוראות.תכנית|תכנית", "plan", 1.0),

mcp-server/src/legal_mcp/services/processor.py

@@ -3,6 +3,7 @@
 from __future__ import annotations
 
 import logging
+from pathlib import Path
 from uuid import UUID
 
 from legal_mcp.services import chunker, db, embeddings, extractor, references_extractor
@@ -37,6 +38,17 @@ async def process_document(document_id: UUID, case_id: UUID) -> dict:
             page_count=page_count,
         )
 
+        # Save extracted text to documents/extracted/ directory
+        original_path = Path(doc["file_path"])
+        extracted_dir = original_path.parent.parent / "extracted"
+        extracted_dir.mkdir(parents=True, exist_ok=True)
+        txt_path = extracted_dir / (original_path.stem + ".txt")
+        try:
+            txt_path.write_text(text, encoding="utf-8")
+            logger.info("Saved extracted text to %s", txt_path)
+        except Exception as e:
+            logger.warning("Failed to save text file (non-fatal): %s", e)
+
         # Step 1.5: Classify document — local rules first, Claude Code headless fallback
         classification_result = {}
         try:

mcp-server/src/legal_mcp/tools/cases.py

@@ -62,7 +62,12 @@ async def case_create(
     # Initialize git repo for the case
     case_dir = config.find_case_dir(case_number)
     case_dir.mkdir(parents=True, exist_ok=True)
-    (case_dir / "documents").mkdir(exist_ok=True)
+    docs_dir = case_dir / "documents"
+    docs_dir.mkdir(exist_ok=True)
+    (docs_dir / "original").mkdir(exist_ok=True)
+    (docs_dir / "extracted").mkdir(exist_ok=True)
+    (docs_dir / "proofread").mkdir(exist_ok=True)
+    (docs_dir / "backup").mkdir(exist_ok=True)
     (case_dir / "drafts").mkdir(exist_ok=True)
 
     # Save case metadata