fix: address review feedback — version check, Set mutation, barrel edge duplication (#634)

- Move _versionWarned flag outside mismatch conditional to avoid
  redundant build_meta queries when versions match.
- Wrap SUPPORTED_EXTENSIONS in new Set() to avoid mutating the
  sibling module's export.
- Delete outgoing edges for barrel-only files before re-adding them
  to fileSymbols during incremental builds, preventing duplicate
  reexport edges.

Author: carlos-alm

src/db/connection.ts

@@ -221,7 +221,7 @@ export function openReadonlyOrFail(customPath?: string): BetterSqlite3Database {
     ) => BetterSqlite3Database
   )(dbPath, { readonly: true });
 
-  // Warn once if the DB was built with a different codegraph version
+  // Warn once per process if the DB was built with a different codegraph version
   if (!_versionWarned) {
     try {
       const row = db
@@ -233,11 +233,11 @@ export function openReadonlyOrFail(customPath?: string): BetterSqlite3Database {
         warn(
           `DB was built with codegraph v${buildVersion}, running v${currentVersion}. Consider: codegraph build --no-incremental`,
         );
-        _versionWarned = true;
       }
     } catch {
       // build_meta table may not exist in older DBs — silently ignore
     }
+    _versionWarned = true;
   }
 
   return db;

src/domain/graph/builder/stages/resolve-imports.ts

@@ -46,13 +46,19 @@ export async function resolveImports(ctx: PipelineContext): Promise<void> {
          JOIN nodes n1 ON e.source_id = n1.id
          WHERE e.kind = 'reexports' AND n1.kind = 'file'`)
       .all() as Array<{ file: string }>;
+    // Barrel-only files will have edges re-created by buildEdges; delete
+    // their outgoing edges first to prevent duplicates during incremental builds.
+    const deleteOutgoingEdges = db.prepare(
+      'DELETE FROM edges WHERE source_id IN (SELECT id FROM nodes WHERE file = ?)',
+    );
     for (const { file: relPath } of barrelCandidates) {
       if (fileSymbols.has(relPath)) continue;
       const absPath = path.join(rootDir, relPath);
       try {
         const symbols = await parseFilesAuto([absPath], rootDir, engineOpts);
         const fileSym = symbols.get(relPath);
         if (fileSym) {
+          deleteOutgoingEdges.run(relPath);
           fileSymbols.set(relPath, fileSym);
           ctx.barrelOnlyFiles.add(relPath);
           const reexports = fileSym.imports.filter((imp: Import) => imp.reexport);

src/shared/constants.ts

@@ -36,7 +36,7 @@ export const IGNORE_DIRS: ArrayCompatSet<string> = withArrayCompat(
   ]),
 );
 
-export const EXTENSIONS: ArrayCompatSet<string> = withArrayCompat(SUPPORTED_EXTENSIONS);
+export const EXTENSIONS: ArrayCompatSet<string> = withArrayCompat(new Set(SUPPORTED_EXTENSIONS));
 
 export function shouldIgnore(dirName: string): boolean {
   return IGNORE_DIRS.has(dirName) || dirName.startsWith('.');