Remove unreachable code and fix two defects it surfaced

Delete repository methods with no callers (SettingsRepository CRUD,
ChunkRepository.update/delete/get_chunks_in_range), the DataFrame branch of
_process_search_results whose only caller always passes a query, and guards
that cannot be reached from their call sites: the rebuild mode=None default,
the staging drop already performed by _resolve_rebuild_recovery, the empty
batch skip, two context fast paths, the doctor prefix guard, the poller
_task attribute that is never assigned, and a docling caption fallback for
a field name no item class defines.

set_haiku_version built a recreated settings row from the process-global
Config rather than the store's own, so a store opened with a custom config
stamped global settings into the database.

check_source_accessible called urlparse outside its try block, so a stored
URI with a malformed IPv6 host raised ValueError instead of reporting the
source as inaccessible, aborting the whole rebuild sweep.

CHANGELOG.md

@@ -1,6 +1,15 @@
 # Changelog
 ## [Unreleased]
 
+### Fixed
+
+- `Store.set_haiku_version` stamps the store's own config into a recreated settings row instead of the process-global `Config`.
+- `check_source_accessible` returns `False` for a URI that fails to parse instead of raising `ValueError`.
+
+### Removed
+
+- `SettingsRepository.create`, `get_by_id`, `update`, `delete`, `list_all` and `ChunkRepository.update`, `delete`, `get_chunks_in_range`.
+
 ## [0.70.0] - 2026-07-25
 
 ### Added

haiku_rag_slim/haiku/rag/client/documents.py

@@ -906,13 +906,17 @@ async def update_document(
 
 
 def check_source_accessible(uri: str) -> bool:
-    """Check if a document's source URI is accessible."""
+    """Check if a document's source URI is accessible.
-    parsed_url = urlparse(uri)
+
+    A stored URI that no longer parses (``urlparse`` rejects malformed IPv6
+    hosts) counts as inaccessible rather than aborting the caller's sweep.
+    """
     try:
+        parsed_url = urlparse(uri)
         if parsed_url.scheme == "file":
             return Path(parsed_url.path).exists()
         elif parsed_url.scheme in ("http", "https", "s3"):
             return True
         return False
-    except Exception:
+    except ValueError:
         return False

haiku_rag_slim/haiku/rag/client/rebuild.py

@@ -66,7 +66,7 @@ class _StagingMarkerRecord(LanceModel):
 
 
 async def rebuild_database(
-    client: "HaikuRAG", mode: "RebuildMode | None" = None
+    client: "HaikuRAG", mode: "RebuildMode"
 ) -> AsyncGenerator[str, None]:
     """Rebuild the database with the specified mode.
 
@@ -79,9 +79,6 @@ async def rebuild_database(
     """
     from haiku.rag.client import RebuildMode
 
-    if mode is None:
-        mode = RebuildMode.FULL
-
     async with client.store._rebuild_lock:
         if mode == RebuildMode.SET_EMBEDDER:
             await _set_embedder(client)
@@ -287,8 +284,6 @@ async def _populate_staging_table(client: "HaikuRAG") -> None:
     """
     db = client.store.db
     tables = (await db.list_tables()).tables
-    if _STAGING_TABLE_NAME in tables:
-        await db.drop_table(_STAGING_TABLE_NAME)
 
     staging = await db.create_table(_STAGING_TABLE_NAME, schema=_StagingChunkRecord)
     if "chunks" not in tables:
@@ -301,8 +296,6 @@ async def _populate_staging_table(client: "HaikuRAG") -> None:
     )
     async for batch in stream:
         rows = batch.to_pylist()
-        if not rows:
-            continue
         records = [
             _StagingChunkRecord(
                 id=r["id"],

haiku_rag_slim/haiku/rag/context.py

@@ -101,8 +101,6 @@ def _evidence_anchors(content: str, max_chars: int) -> list[str]:
             mid = len(content) // 2
             start = max(0, mid - target // 2)
             anchors.append(content[start : start + target])
-    if not anchors:
-        anchors.append(content[:max_chars] if max_chars > 0 else content)
     return anchors
 
 
@@ -289,8 +287,6 @@ def _add_input_pages_for_surviving_refs(
 ) -> None:
     """Fill missing item-table pages from inputs whose own refs all survived."""
     surviving = set(refs)
-    if not surviving:
-        return
     for result in original_results:
         if not result.page_numbers or not result.doc_item_refs:
             continue

haiku_rag_slim/haiku/rag/doctor.py

@@ -330,8 +330,6 @@ def _common_path_prefix(labels: list[str]) -> str:
     Returns "" unless the shared prefix is long enough to be worth factoring out
     of every line (deep URI trees are otherwise unreadable).
     """
-    if len(labels) < 2:
-        return ""
     lo, hi = min(labels), max(labels)
     end = 0
     while end < len(lo) and lo[end] == hi[end]:

haiku_rag_slim/haiku/rag/ingester/pollers/base.py

@@ -55,7 +55,6 @@ class BasePoller:
         self._sync = sync_repo
         self._breaker = breaker or CircuitBreaker(config.circuit_breaker)
         self._stop = asyncio.Event()
-        self._task: asyncio.Task | None = None
         self._last_polled_at: datetime | None = None
         self._last_skip_reason: str | None = None
         self._default_max_attempts = default_max_attempts
@@ -84,9 +83,6 @@ class BasePoller:
 
     async def stop(self) -> None:
         self._stop.set()
-        if self._task is not None:
-            await asyncio.gather(self._task, return_exceptions=True)
-            self._task = None
 
     async def _stagger_start(self) -> bool:
         """Sleep a random fraction of the interval so pollers sharing an

haiku_rag_slim/haiku/rag/store/engine.py

@@ -847,7 +847,7 @@ class Store:
                 )
         else:
             # Create new settings record
-            settings_data = Config.model_dump(mode="json")
+            settings_data = self._config.model_dump(mode="json")
             settings_data["version"] = version
             await self.settings_table.add(
                 [SettingsRecord(id="settings", settings=json.dumps(settings_data))]

haiku_rag_slim/haiku/rag/store/models/document_item.py

@@ -105,10 +105,6 @@ def extract_item_text(
         except Exception:
             pass
 
-    if caption := getattr(item, "caption", None):
-        if hasattr(caption, "text"):
-            return caption.text
-
     return None
 
 

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

@@ -4,7 +4,6 @@ from typing import TYPE_CHECKING
 from uuid import uuid4
 
 if TYPE_CHECKING:
-    import pandas as pd
     from lancedb.query import AsyncQueryBase
 
 from lancedb.index import FTS
@@ -153,40 +152,6 @@ class ChunkRepository:
             order=chunk_record.order,
         )
 
-    async def update(self, entity: Chunk) -> Chunk:
-        """Update an existing chunk.
-
-        Chunk must have embedding set before calling this method.
-        """
-        self.store._assert_writable()
-        assert entity.id, "Chunk ID is required for update"
-        assert entity.embedding is not None, "Chunk must have an embedding"
-
-        await self.store.chunks_table.update(
-            {
-                "document_id": entity.document_id,
-                "content": entity.content,
-                "content_fts": self._contextualize_content(entity),
-                "metadata": json.dumps(
-                    {k: v for k, v in entity.metadata.items() if k != "order"}
-                ),
-                "order": int(entity.order),
-                "vector": entity.embedding,
-            },
-            where=f"id = '{entity.id}'",
-        )
-        return entity
-
-    async def delete(self, entity_id: str) -> bool:
-        """Delete a chunk by its ID."""
-        self.store._assert_writable()
-        chunk = await self.get_by_id(entity_id)
-        if chunk is None:
-            return False
-
-        await self.store.chunks_table.delete(f"id = '{entity_id}'")
-        return True
-
     async def list_all(
         self, limit: int | None = None, offset: int | None = None
     ) -> list[Chunk]:
@@ -417,46 +382,10 @@ class ChunkRepository:
         )
         return len(df)
 
-    async def get_chunks_in_range(
-        self, document_id: str, min_order: int, max_order: int
-    ) -> list[Chunk]:
-        """Get chunks for a document within an order range.
-
-        Args:
-            document_id: The document ID to get chunks for.
-            min_order: Minimum order value (inclusive).
-            max_order: Maximum order value (inclusive).
-
-        Returns:
-            List of chunks within the order range.
-        """
-        where = (
-            f"document_id = '{document_id}'"
-            f" AND `order` >= {min_order}"
-            f" AND `order` <= {max_order}"
-        )
-        results = await query_to_pydantic(
-            self.store.chunks_table.query().where(where), self.store.ChunkRecord
-        )
-        return [
-            Chunk(
-                id=rec.id,
-                document_id=rec.document_id,
-                content=rec.content,
-                metadata=json.loads(rec.metadata),
-                order=rec.order,
-            )
-            for rec in results
-        ]
-
     async def _process_search_results(
-        self, query_result: "pd.DataFrame | AsyncQueryBase"
+        self, query_result: "AsyncQueryBase"
     ) -> list[tuple[Chunk, float]]:
-        """Process search results into chunks with document info and scores.
+        """Process search results into chunks with document info and scores."""
-
-        Args:
-            query_result: Either a pandas DataFrame or a LanceDB async query result
-        """
         import pandas as pd
 
         def extract_scores(df: pd.DataFrame) -> list[float]:
@@ -473,11 +402,6 @@ class ChunkRepository:
             else:
                 raise ValueError("Unknown search result format, cannot extract scores")
 
-        # Convert everything to DataFrame for uniform processing
-        if isinstance(query_result, pd.DataFrame):
-            df = query_result
-        else:
-            # Convert LanceDB query result to DataFrame
         df = await query_result.to_pandas()
 
         # Extract scores

haiku_rag_slim/haiku/rag/store/repositories/settings.py

@@ -18,47 +18,6 @@ class SettingsRepository:
     def __init__(self, store: Store) -> None:
         self.store = store
 
-    async def create(self, entity: dict) -> dict:
-        """Create settings in the database."""
-        settings_record = SettingsRecord(id="settings", settings=json.dumps(entity))
-        await self.store.settings_table.add([settings_record])
-        return entity
-
-    async def get_by_id(self, entity_id: str) -> dict | None:
-        """Get settings by ID."""
-        results = await query_to_pydantic(
-            self.store.settings_table.query().where(f"id = '{entity_id}'").limit(1),
-            SettingsRecord,
-        )
-
-        if not results:
-            return None
-
-        return json.loads(results[0].settings) if results[0].settings else {}
-
-    async def update(self, entity: dict) -> dict:
-        """Update existing settings."""
-        await self.store.settings_table.update(
-            {"settings": json.dumps(entity)}, where="id = 'settings'"
-        )
-        return entity
-
-    async def delete(self, entity_id: str) -> bool:
-        """Delete settings by ID."""
-        await self.store.settings_table.delete(f"id = '{entity_id}'")
-        return True
-
-    async def list_all(
-        self, limit: int | None = None, offset: int | None = None
-    ) -> list[dict]:
-        """List all settings."""
-        results = await query_to_pydantic(
-            self.store.settings_table.query(), SettingsRecord
-        )
-        return [
-            json.loads(record.settings) if record.settings else {} for record in results
-        ]
-
     async def get_current_settings(self) -> dict:
         """Get the current settings."""
         results = await query_to_pydantic(

tests/test_client.py

@@ -14,6 +14,7 @@ from haiku.rag.client.documents import (
     DocumentImport,
     _prepare_document_from_docling,
     _write_fetch_body,
+    check_source_accessible,
 )
 from haiku.rag.config import Config
 from haiku.rag.store.compression import decompress_json
@@ -2254,3 +2255,27 @@ async def test_metadata_only_update_waits_for_write_lock(temp_db_path):
             assert not task.done()
         updated = await task
         assert updated.metadata == {"k": "v"}
+
+
+@pytest.mark.parametrize(
+    "uri,expected",
+    [
+        ("https://example.com/doc.pdf", True),
+        ("s3://bucket/key", True),
+        ("mem://not-a-source", False),
+        # urlparse rejects a malformed IPv6 host; a stored URI that no longer
+        # parses must not abort the caller's rebuild sweep.
+        ("http://[::1", False),
+    ],
+    ids=["https", "s3", "unknown_scheme", "unparseable"],
+)
+def test_check_source_accessible(uri, expected):
+    assert check_source_accessible(uri) is expected
+
+
+def test_check_source_accessible_file_uri(tmp_path):
+    existing = tmp_path / "there.txt"
+    existing.write_text("x")
+
+    assert check_source_accessible(existing.as_uri()) is True
+    assert check_source_accessible((tmp_path / "gone.txt").as_uri()) is False

tests/test_settings.py

@@ -44,6 +44,31 @@ async def test_settings_save_and_retrieve(temp_db_path):
         Config.processing.chunk_size = original_chunk_size
 
 
+@pytest.mark.asyncio
+async def test_set_haiku_version_recreates_row_from_store_config(temp_db_path):
+    """Recreating a missing settings row stamps the store's own config, not the
+    process-global one."""
+    from haiku.rag.store.engine import Store
+    from haiku.rag.store.repositories.settings import SettingsRepository
+
+    config = AppConfig()
+    config.processing.chunk_size = Config.processing.chunk_size + 512
+
+    async with Store(temp_db_path, config=config, create=True) as store:
+        settings_repo = SettingsRepository(store)
+
+        await store.settings_table.delete("id = 'settings'")
+        assert await settings_repo.get_current_settings() == {}
+        assert await store.get_haiku_version() == "0.0.0"
+
+        await store.set_haiku_version("1.2.3")
+
+        recreated = await settings_repo.get_current_settings()
+        assert recreated["version"] == "1.2.3"
+        assert recreated["processing"]["chunk_size"] == config.processing.chunk_size
+        assert await store.get_haiku_version() == "1.2.3"
+
+
 class TestValidateConfigCompatibility:
     """Tests for validate_config_compatibility method."""