Upgrade fts index for phrase queries

src/haiku/rag/store/engine.py

@@ -118,8 +118,10 @@ class Store:
             self.chunks_table = self.db.open_table("chunks")
         else:
             self.chunks_table = self.db.create_table("chunks", schema=self.ChunkRecord)
-            # Create FTS index on the new table
-            self.chunks_table.create_fts_index("content", replace=True)
+            # Create FTS index on the new table with phrase query support
+            self.chunks_table.create_fts_index(
+                "content", replace=True, with_position=True, remove_stop_words=False
+            )
 
         # Create or get settings table
         if "settings" in existing_tables:
@@ -222,8 +224,10 @@ class Store:
         self.ChunkRecord = create_chunk_model(self.embedder._vector_dim)
         self.chunks_table = self.db.create_table("chunks", schema=self.ChunkRecord)
 
-        # Create FTS index on the new table
-        self.chunks_table.create_fts_index("content", replace=True)
+        # Create FTS index on the new table with phrase query support
+        self.chunks_table.create_fts_index(
+            "content", replace=True, with_position=True, remove_stop_words=False
+        )
 
     def close(self):
         """Close the database connection."""

src/haiku/rag/store/repositories/chunk.py

@@ -28,7 +28,9 @@ class ChunkRepository:
     def _ensure_fts_index(self) -> None:
         """Ensure FTS index exists on the content column."""
         try:
-            self.store.chunks_table.create_fts_index("content", replace=True)
+            self.store.chunks_table.create_fts_index(
+                "content", replace=True, with_position=True, remove_stop_words=False
+            )
         except Exception as e:
             # Log the error but don't fail - FTS might already exist
             logger.debug(f"FTS index creation skipped: {e}")
@@ -236,8 +238,10 @@ class ChunkRepository:
         self.store.chunks_table = self.store.db.create_table(
             "chunks", schema=self.store.ChunkRecord
         )
-        # Create FTS index on the new table
-        self.store.chunks_table.create_fts_index("content", replace=True)
+        # Create FTS index on the new table with phrase query support
+        self.store.chunks_table.create_fts_index(
+            "content", replace=True, with_position=True, remove_stop_words=False
+        )
 
     async def delete_by_document_id(self, document_id: str) -> bool:
         """Delete all chunks for a document."""

src/haiku/rag/store/upgrades/__init__.py

@@ -1,5 +1,4 @@
-from __future__ import annotations
-
+import logging
 from collections.abc import Callable
 from dataclasses import dataclass
 
@@ -7,6 +6,8 @@ from packaging.version import Version, parse
 
 from haiku.rag.store.engine import Store
 
+logger = logging.getLogger(__name__)
+
 
 @dataclass
 class Upgrade:
@@ -33,14 +34,27 @@ def run_pending_upgrades(store: Store, from_version: str, to_version: str) -> No
         if highest_step_version > v_to:
             v_to = highest_step_version
 
-    # Ensure upgrades are applied in ascending version order
-    for step in sorted(upgrades, key=lambda u: parse(u.version)):
-        v_step = parse(step.version)
-        if v_from < v_step <= v_to:
-            step.apply(store)
+    # Determine applicable steps
+    sorted_steps = sorted(upgrades, key=lambda u: parse(u.version))
+    applicable = [s for s in sorted_steps if v_from < parse(s.version) <= v_to]
+    if applicable:
+        logger.info("%d upgrade step(s) pending", len(applicable))
+
+    # Apply in ascending order
+    for idx, step in enumerate(applicable, start=1):
+        logger.info(
+            "Applying upgrade %s: %s (%d/%d)",
+            step.version,
+            step.description or "",
+            idx,
+            len(applicable),
+        )
+        step.apply(store)
+        logger.info("Completed upgrade %s", step.version)
 
 
-# Import concrete upgrade modules (module names cannot start with a digit)
+from .v0_9_3 import upgrade_fts_phrase as upgrade_0_9_3_fts  # noqa: E402
 from .v0_9_3 import upgrade_order as upgrade_0_9_3_order  # noqa: E402
 
 upgrades.append(upgrade_0_9_3_order)
+upgrades.append(upgrade_0_9_3_fts)

src/haiku/rag/store/upgrades/v0_9_3.py

@@ -1,15 +1,10 @@
-from __future__ import annotations
-
 import json
-from typing import TYPE_CHECKING
 
 from lancedb.pydantic import LanceModel, Vector
 from pydantic import Field
 
-from . import Upgrade
-
-if TYPE_CHECKING:  # pragma: no cover - for type hints only
-    from haiku.rag.store.engine import Store
+from haiku.rag.store.engine import Store
+from haiku.rag.store.upgrades import Upgrade
 
 
 def _infer_vector_dim(store: Store) -> int:
@@ -32,7 +27,6 @@ def _apply_chunk_order(store: Store) -> None:
 
     vector_dim = _infer_vector_dim(store)
 
-    # ============== Chunks: add 'order' column and backfill ==============
     class ChunkRecordV2(LanceModel):
         id: str
         document_id: str
@@ -88,7 +82,6 @@ def _apply_chunk_order(store: Store) -> None:
         pass
 
     store.chunks_table = store.db.create_table("chunks", schema=ChunkRecordV2)
-    # Recreate FTS index on content
     store.chunks_table.create_fts_index("content", replace=True)
 
     if new_chunk_records:
@@ -100,3 +93,20 @@ upgrade_order = Upgrade(
     apply=_apply_chunk_order,
     description="Add 'order' column to chunks and backfill from metadata",
 )
+
+
+def _apply_fts_phrase_support(store: Store) -> None:
+    """Recreate FTS index with phrase query support and no stop-word removal."""
+    try:
+        store.chunks_table.create_fts_index(
+            "content", replace=True, with_position=True, remove_stop_words=False
+        )
+    except Exception:
+        pass
+
+
+upgrade_fts_phrase = Upgrade(
+    version="0.9.3",
+    apply=_apply_fts_phrase_support,
+    description="Enable FTS phrase queries (with positions) and keep stop-words",
+)