perf(db): batch node lookups, fix insertNode cache, run maintenance after writes (#108)

Batch getNodesByIds to collapse N+1 reads in graph traversal, invalidate the
insertNode LRU cache so INSERT OR REPLACE doesn't serve a stale row, and run
incremental PRAGMA optimize + passive WAL checkpoint after bulk writes.

Closes #108

src/index.ts

@@ -347,6 +347,12 @@ export class CodeGraph {
           });
         }
 
+        // Refresh planner stats + checkpoint the WAL after bulk writes.
+        // Cheap and non-blocking; never load-bearing for correctness.
+        if (result.success && result.filesIndexed > 0) {
+          this.db.runMaintenance();
+        }
+
         return result;
       } finally {
         this.fileLock.release();
@@ -428,6 +434,11 @@ export class CodeGraph {
           }
         }
 
+        // Refresh planner stats + checkpoint the WAL after bulk writes.
+        if (result.filesAdded > 0 || result.filesModified > 0 || result.filesRemoved > 0) {
+          this.db.runMaintenance();
+        }
+
         return result;
       } finally {
         this.fileLock.release();