fix(storage): index the columns behind ON DELETE SET NULL

CHANGELOG.md

@@ -6,6 +6,13 @@ All notable changes to this project are documented here. The format is based on
 
 ## [Unreleased]
 
+### Fixed
+
+- Removing files from a large index no longer takes hours: `chunks.symbol_id` and
+  `symbols.parent_id` are now indexed, so a deleted symbol no longer costs a full scan
+  of both tables. Existing indexes gain the two indexes the next time they are opened,
+  with no rebuild.
+
 ## [2.1.2] - 2026-09-25
 
 ### Fixed

docs/SCHEMA.md

@@ -44,6 +44,7 @@ CREATE TABLE chunks (
     symbol_names  TEXT NOT NULL DEFAULT ''     -- denormalized symbol name, FTS-indexed (mirrored by triggers)
 );
 CREATE INDEX idx_chunks_file ON chunks(file_id);
+CREATE INDEX idx_chunks_symbol ON chunks(symbol_id);
 
 -- Symbols extracted via tree-sitter (definitions).
 CREATE TABLE symbols (
@@ -63,6 +64,7 @@ CREATE TABLE symbols (
 CREATE INDEX idx_symbols_name ON symbols(name);
 CREATE INDEX idx_symbols_file ON symbols(file_id);
 CREATE INDEX idx_symbols_kind ON symbols(kind);
+CREATE INDEX idx_symbols_parent ON symbols(parent_id);
 
 -- Graph edges: imports / calls / references / inheritance / dependencies.
 -- src is always a known symbol or file; dst may be unresolved (dst_id NULL, dst_name kept).

src/codebase_index/storage/schema.sql

@@ -35,6 +35,9 @@ CREATE TABLE IF NOT EXISTS symbols (
 CREATE INDEX IF NOT EXISTS idx_symbols_name ON symbols(name);
 CREATE INDEX IF NOT EXISTS idx_symbols_file ON symbols(file_id);
 CREATE INDEX IF NOT EXISTS idx_symbols_kind ON symbols(kind);
+-- Every deleted symbol looks up its children for ON DELETE SET NULL here and on
+-- chunks.symbol_id; without an index each lookup is a full table scan.
+CREATE INDEX IF NOT EXISTS idx_symbols_parent ON symbols(parent_id);
 
 CREATE TABLE IF NOT EXISTS chunks (
     id            INTEGER PRIMARY KEY,
@@ -52,6 +55,7 @@ CREATE TABLE IF NOT EXISTS chunks (
     symbol_names  TEXT NOT NULL DEFAULT ''
 );
 CREATE INDEX IF NOT EXISTS idx_chunks_file ON chunks(file_id);
+CREATE INDEX IF NOT EXISTS idx_chunks_symbol ON chunks(symbol_id);
 
 CREATE TABLE IF NOT EXISTS edges (
     id            INTEGER PRIMARY KEY,

tests/test_storage.py

@@ -42,6 +42,35 @@ def test_future_schema_version_raises(tmp_path):
             pass
 
 
+def test_every_foreign_key_column_leads_an_index(tmp_path):
+    """Without one, SQLite scans the child table for every deleted parent row."""
+    with Database(tmp_path / "index.sqlite") as db:
+        conn = db.conn
+        tables = [
+            r[0]
+            for r in conn.execute(
+                "SELECT name FROM sqlite_master WHERE type='table' AND name NOT LIKE 'fts_%'"
+            )
+        ]
+        for table in tables:
+            leading = {
+                conn.execute(f"PRAGMA index_info({index['name']})").fetchone()["name"]
+                for index in conn.execute(f"PRAGMA index_list({table})").fetchall()
+            }
+            for fk in conn.execute(f"PRAGMA foreign_key_list({table})").fetchall():
+                assert fk["from"] in leading, f"{table}.{fk['from']} has no index"
+
+
+def test_existing_index_gains_new_indexes_on_open(tmp_path):
+    db_path = tmp_path / "index.sqlite"
+    with Database(db_path) as db:
+        db.conn.execute("DROP INDEX idx_chunks_symbol")
+        db.conn.execute("DROP INDEX idx_symbols_parent")
+    with Database(db_path) as db:
+        names = {r[0] for r in db.conn.execute("SELECT name FROM sqlite_master WHERE type='index'")}
+    assert {"idx_chunks_symbol", "idx_symbols_parent"} <= names
+
+
 def _open(tmp_path):
     return Database(tmp_path / "index.sqlite").open()