fix(indexer): write sync-result.json in reindex() not just sync()

reindex() was consuming the full_index() generator but never calling
_write_sync_result(), leaving sync-result.json stale while CLI output
showed correct indexed_files/total_chunks.

python/obsidian_rag/indexer.py

@@ -4,8 +4,6 @@ from __future__ import annotations
 
 import json
 import os
-import time
-import uuid
 from datetime import datetime, timezone
 from pathlib import Path
 from typing import TYPE_CHECKING, Any, Generator, Iterator
@@ -16,10 +14,13 @@ if TYPE_CHECKING:
 import obsidian_rag.config as config_mod
 from obsidian_rag.config import _resolve_data_dir
 from obsidian_rag.chunker import chunk_file
-from obsidian_rag.embedder import EmbeddingError, OllamaUnavailableError, SecurityError
+from obsidian_rag.embedder import OllamaUnavailableError
 from obsidian_rag.security import should_index_dir, validate_path
-from obsidian_rag.audit_logger import AuditLogger
-from obsidian_rag.vector_store import create_table_if_not_exists, delete_by_source_file, get_db, upsert_chunks
+from obsidian_rag.vector_store import (
+    create_table_if_not_exists,
+    get_db,
+    upsert_chunks,
+)
 
 # ----------------------------------------------------------------------
 # Pipeline
@@ -43,6 +44,7 @@ class Indexer:
     def embedder(self):
         if self._embedder is None:
             from obsidian_rag.embedder import OllamaEmbedder
+
             self._embedder = OllamaEmbedder(self.config)
         return self._embedder
 
@@ -50,6 +52,7 @@ class Indexer:
     def audit_logger(self):
         if self._audit_logger is None:
             from obsidian_rag.audit_logger import AuditLogger
+
             log_dir = _resolve_data_dir() / "audit"
             self._audit_logger = AuditLogger(log_dir / "audit.log")
         return self._audit_logger
@@ -57,18 +60,18 @@ class Indexer:
     def _check_sensitive_content_approval(self, chunks: list[dict[str, Any]]) -> None:
         """Enforce user approval for sensitive content before indexing."""
         from obsidian_rag import security
-        
+
         sensitive_categories = self.config.security.require_confirmation_for
         if not sensitive_categories:
             return
-        
+
         for chunk in chunks:
             sensitivity = security.detect_sensitive(
-                chunk['chunk_text'],
+                chunk["chunk_text"],
                 self.config.security.sensitive_sections,
-                self.config.memory.patterns
+                self.config.memory.patterns,
             )
-            
+
             for category in sensitive_categories:
                 if sensitivity.get(category, False):
                     if not self.config.security.auto_approve_sensitive:
@@ -99,7 +102,11 @@ class Indexer:
         """Index a single file. Returns (num_chunks, enriched_chunks)."""
         from obsidian_rag import security
 
-        mtime = str(datetime.fromtimestamp(filepath.stat().st_mtime, tz=timezone.utc).isoformat())
+        mtime = str(
+            datetime.fromtimestamp(
+                filepath.stat().st_mtime, tz=timezone.utc
+            ).isoformat()
+        )
         content = filepath.read_text(encoding="utf-8")
         # Sanitize
         content = security.sanitize_text(content)
@@ -147,24 +154,25 @@ class Indexer:
                 num_chunks, enriched = self.process_file(filepath)
                 # Enforce sensitive content policies
                 self._check_sensitive_content_approval(enriched)
-                
+
                 # Log sensitive content access
                 for chunk in enriched:
                     from obsidian_rag import security
+
                     sensitivity = security.detect_sensitive(
-                        chunk['chunk_text'],
+                        chunk["chunk_text"],
                         self.config.security.sensitive_sections,
-                        self.config.memory.patterns
+                        self.config.memory.patterns,
                     )
-                    for category in ['health', 'financial', 'relations']:
+                    for category in ["health", "financial", "relations"]:
                         if sensitivity.get(category, False):
                             self.audit_logger.log_sensitive_access(
-                                str(chunk['source_file']),
+                                str(chunk["source_file"]),
                                 category,
-                                'index',
-                                {'chunk_id': chunk['chunk_id']}
+                                "index",
+                                {"chunk_id": chunk["chunk_id"]},
                             )
-                
+
                 # Embed chunks
                 texts = [e["chunk_text"] for e in enriched]
                 try:
@@ -249,9 +257,16 @@ class Indexer:
         db = get_db(self.config)
         if "obsidian_chunks" in db.list_tables():
             db.drop_table("obsidian_chunks")
-        # full_index is a generator — materialize it to get the final dict
         results = list(self.full_index())
-        return results[-1] if results else {"indexed_files": 0, "total_chunks": 0, "errors": []}
+        final = (
+            results[-1]
+            if results
+            else {"indexed_files": 0, "total_chunks": 0, "errors": []}
+        )
+        self._write_sync_result(
+            final["indexed_files"], final["total_chunks"], final["errors"]
+        )
+        return final
 
     def _sync_result_path(self) -> Path:
         # Use the same dev-data-dir convention as config.py
@@ -309,24 +324,25 @@ class Indexer:
                 num_chunks, enriched = self.process_file(filepath)
                 # Enforce sensitive content policies
                 self._check_sensitive_content_approval(enriched)
-                
+
                 # Log sensitive content access
                 for chunk in enriched:
                     from obsidian_rag import security
+
                     sensitivity = security.detect_sensitive(
-                        chunk['chunk_text'],
+                        chunk["chunk_text"],
                         self.config.security.sensitive_sections,
-                        self.config.memory.patterns
+                        self.config.memory.patterns,
                     )
-                    for category in ['health', 'financial', 'relations']:
+                    for category in ["health", "financial", "relations"]:
                         if sensitivity.get(category, False):
                             self.audit_logger.log_sensitive_access(
-                                str(chunk['source_file']),
+                                str(chunk["source_file"]),
                                 category,
-                                'index',
-                                {'chunk_id': chunk['chunk_id']}
+                                "index",
+                                {"chunk_id": chunk["chunk_id"]},
                             )
-                
+
                 # Embed chunks
                 texts = [e["chunk_text"] for e in enriched]
                 try:
@@ -353,4 +369,3 @@ class Indexer:
         if not data_dir.exists() and not (project_root / "KnowledgeVault").exists():
             data_dir = Path(os.path.expanduser("~/.obsidian-rag"))
         return data_dir / "sync-result.json"
-