Enhance search functionality and indexing pipeline

- Updated `cmd_search` to include line numbers and content in search results.
- Modified `IndexingPipeline` to handle start and end line numbers for chunks.
- Enhanced `FTSEngine` to support storing line metadata in the database.
- Improved `SearchPipeline` to return line numbers and full content in search results.
- Added unit tests for bridge, FTS delete operations, metadata store, and watcher functionality.
- Introduced a `.gitignore` file to exclude specific directories.

codex-lens-v2/tests/unit/test_metadata_store.py

@@ -0,0 +1,184 @@
+"""Unit tests for MetadataStore — SQLite file-to-chunk mapping + tombstone tracking."""
+from __future__ import annotations
+
+import pytest
+
+from codexlens_search.indexing.metadata import MetadataStore
+
+
+@pytest.fixture
+def store(tmp_path):
+    """Create a fresh MetadataStore backed by a temp db."""
+    return MetadataStore(str(tmp_path / "meta.db"))
+
+
+# ---------------------------------------------------------------------------
+# Table creation
+# ---------------------------------------------------------------------------
+
+class TestTableCreation:
+    def test_creates_three_tables(self, store):
+        """MetadataStore should create files, chunks, deleted_chunks tables."""
+        tables = store._conn.execute(
+            "SELECT name FROM sqlite_master WHERE type='table' ORDER BY name"
+        ).fetchall()
+        names = {r[0] for r in tables}
+        assert "files" in names
+        assert "chunks" in names
+        assert "deleted_chunks" in names
+
+    def test_foreign_keys_enabled(self, store):
+        """PRAGMA foreign_keys must be ON."""
+        row = store._conn.execute("PRAGMA foreign_keys").fetchone()
+        assert row[0] == 1
+
+    def test_wal_mode(self, store):
+        """journal_mode should be WAL for concurrency."""
+        row = store._conn.execute("PRAGMA journal_mode").fetchone()
+        assert row[0].lower() == "wal"
+
+
+# ---------------------------------------------------------------------------
+# register_file
+# ---------------------------------------------------------------------------
+
+class TestRegisterFile:
+    def test_register_and_retrieve(self, store):
+        store.register_file("src/main.py", "abc123", 1000.0)
+        assert store.get_file_hash("src/main.py") == "abc123"
+
+    def test_register_updates_existing(self, store):
+        store.register_file("a.py", "hash1", 1000.0)
+        store.register_file("a.py", "hash2", 2000.0)
+        assert store.get_file_hash("a.py") == "hash2"
+
+    def test_get_file_hash_returns_none_for_unknown(self, store):
+        assert store.get_file_hash("nonexistent.py") is None
+
+
+# ---------------------------------------------------------------------------
+# register_chunks
+# ---------------------------------------------------------------------------
+
+class TestRegisterChunks:
+    def test_register_and_retrieve_chunks(self, store):
+        store.register_file("a.py", "h", 1.0)
+        store.register_chunks("a.py", [(0, "c0"), (1, "c1"), (2, "c2")])
+        ids = store.get_chunk_ids_for_file("a.py")
+        assert sorted(ids) == [0, 1, 2]
+
+    def test_empty_chunks_list(self, store):
+        store.register_file("a.py", "h", 1.0)
+        store.register_chunks("a.py", [])
+        assert store.get_chunk_ids_for_file("a.py") == []
+
+    def test_chunks_for_unknown_file(self, store):
+        assert store.get_chunk_ids_for_file("unknown.py") == []
+
+
+# ---------------------------------------------------------------------------
+# mark_file_deleted
+# ---------------------------------------------------------------------------
+
+class TestMarkFileDeleted:
+    def test_tombstones_chunks(self, store):
+        store.register_file("a.py", "h", 1.0)
+        store.register_chunks("a.py", [(10, "c10"), (11, "c11")])
+        count = store.mark_file_deleted("a.py")
+        assert count == 2
+        assert store.get_deleted_ids() == {10, 11}
+
+    def test_file_removed_after_delete(self, store):
+        store.register_file("a.py", "h", 1.0)
+        store.register_chunks("a.py", [(0, "c0")])
+        store.mark_file_deleted("a.py")
+        assert store.get_file_hash("a.py") is None
+
+    def test_chunks_cascaded_after_delete(self, store):
+        store.register_file("a.py", "h", 1.0)
+        store.register_chunks("a.py", [(0, "c0")])
+        store.mark_file_deleted("a.py")
+        assert store.get_chunk_ids_for_file("a.py") == []
+
+    def test_delete_nonexistent_file(self, store):
+        count = store.mark_file_deleted("nonexistent.py")
+        assert count == 0
+
+    def test_delete_file_without_chunks(self, store):
+        store.register_file("empty.py", "h", 1.0)
+        count = store.mark_file_deleted("empty.py")
+        assert count == 0
+        assert store.get_file_hash("empty.py") is None
+
+
+# ---------------------------------------------------------------------------
+# file_needs_update
+# ---------------------------------------------------------------------------
+
+class TestFileNeedsUpdate:
+    def test_new_file_needs_update(self, store):
+        assert store.file_needs_update("new.py", "any_hash") is True
+
+    def test_unchanged_file(self, store):
+        store.register_file("a.py", "same_hash", 1.0)
+        assert store.file_needs_update("a.py", "same_hash") is False
+
+    def test_changed_file(self, store):
+        store.register_file("a.py", "old_hash", 1.0)
+        assert store.file_needs_update("a.py", "new_hash") is True
+
+
+# ---------------------------------------------------------------------------
+# get_deleted_ids / compact_deleted
+# ---------------------------------------------------------------------------
+
+class TestDeletedIdsAndCompact:
+    def test_empty_deleted_ids(self, store):
+        assert store.get_deleted_ids() == set()
+
+    def test_compact_returns_and_clears(self, store):
+        store.register_file("a.py", "h", 1.0)
+        store.register_chunks("a.py", [(5, "c5"), (6, "c6")])
+        store.mark_file_deleted("a.py")
+
+        deleted = store.compact_deleted()
+        assert deleted == {5, 6}
+        assert store.get_deleted_ids() == set()
+
+    def test_compact_noop_when_empty(self, store):
+        deleted = store.compact_deleted()
+        assert deleted == set()
+
+
+# ---------------------------------------------------------------------------
+# get_all_files / max_chunk_id
+# ---------------------------------------------------------------------------
+
+class TestHelpers:
+    def test_get_all_files(self, store):
+        store.register_file("a.py", "h1", 1.0)
+        store.register_file("b.py", "h2", 2.0)
+        assert store.get_all_files() == {"a.py": "h1", "b.py": "h2"}
+
+    def test_max_chunk_id_empty(self, store):
+        assert store.max_chunk_id() == -1
+
+    def test_max_chunk_id_active(self, store):
+        store.register_file("a.py", "h", 1.0)
+        store.register_chunks("a.py", [(0, "c"), (5, "c"), (3, "c")])
+        assert store.max_chunk_id() == 5
+
+    def test_max_chunk_id_includes_deleted(self, store):
+        store.register_file("a.py", "h", 1.0)
+        store.register_chunks("a.py", [(10, "c")])
+        store.mark_file_deleted("a.py")
+        assert store.max_chunk_id() == 10
+
+    def test_max_chunk_id_mixed(self, store):
+        store.register_file("a.py", "h", 1.0)
+        store.register_chunks("a.py", [(3, "c")])
+        store.register_file("b.py", "h2", 1.0)
+        store.register_chunks("b.py", [(7, "c")])
+        store.mark_file_deleted("a.py")
+        # deleted has 3, active has 7
+        assert store.max_chunk_id() == 7