fix(native): purge stale rows when WASM-only files are deleted

src/domain/graph/builder/pipeline.ts

@@ -15,6 +15,7 @@ import {
   initSchema,
   MIGRATIONS,
   openDb,
+  purgeFilesData,
   releaseAdvisoryLock,
   setBuildMeta,
 } from '../../../db/index.js';
@@ -38,6 +39,7 @@ import {
   formatDropExtensionSummary,
   getActiveEngine,
   getInstalledWasmExtensions,
+  NATIVE_SUPPORTED_EXTENSIONS,
   parseFilesWasmForBackfill,
 } from '../../parser.js';
 import { writeJournalHeader } from '../journal.js';
@@ -774,6 +776,58 @@ async function tryNativeOrchestrator(
   return formatNativeTimingResult(p, structurePatchMs, analysisTiming);
 }
 
+/**
+ * Inputs to {@link computeWasmOnlyStaleFiles}. Sets are passed in so the helper
+ * is pure and unit-testable independently of `getInstalledWasmExtensions` and
+ * the `NATIVE_SUPPORTED_EXTENSIONS` global state.
+ */
+export interface WasmOnlyStaleFilesInput {
+  /** Distinct `file` values from the `nodes` table. */
+  existingNodes: ReadonlySet<string>;
+  /** Distinct `file` values from the `file_hashes` table. */
+  existingHashes: ReadonlySet<string>;
+  /** Relative paths currently on disk (from `collectFilesUtil`). */
+  expected: ReadonlySet<string>;
+  /** Lowercased extensions whose WASM grammar is installed. */
+  installedExts: ReadonlySet<string>;
+  /** Extensions covered by the Rust addon — Rust owns deletion for these. */
+  nativeSupported: ReadonlySet<string>;
+}
+
+/**
+ * Compute the WASM-only files present in the DB but missing from disk (#1073).
+ *
+ * Returns relative paths that:
+ *   - appear in `existingNodes` or `existingHashes` (in DB),
+ *   - are absent from `expected` (not on disk),
+ *   - have an extension installed for WASM, AND
+ *   - have an extension NOT covered by `nativeSupported` — Rust's
+ *     `purge_changed_files` handles deletion for natively-supported extensions
+ *     via its own `detect_removed_files`, so the caller must not double-purge.
+ *
+ * Extensions are lowercased before lookup to match the registry and Rust's
+ * `LanguageKind::from_extension` (which normalises case for the languages
+ * where both cases are conventional, e.g. R's `.r` / `.R`).
+ *
+ * Exported for unit testing.
+ */
+export function computeWasmOnlyStaleFiles(input: WasmOnlyStaleFilesInput): string[] {
+  const { existingNodes, existingHashes, expected, installedExts, nativeSupported } = input;
+  const stale: string[] = [];
+  const seen = new Set<string>();
+  const consider = (rel: string): void => {
+    if (expected.has(rel) || seen.has(rel)) return;
+    const ext = path.extname(rel).toLowerCase();
+    if (nativeSupported.has(ext)) return;
+    if (!installedExts.has(ext)) return;
+    seen.add(rel);
+    stale.push(rel);
+  };
+  for (const rel of existingNodes) consider(rel);
+  for (const rel of existingHashes) consider(rel);
+  return stale;
+}
+
 /**
  * Backfill files that the native orchestrator silently dropped during parse.
  * Falls back to WASM + inserts file/symbol nodes so engine counts match (#967).
@@ -830,7 +884,22 @@ async function backfillNativeDroppedFiles(ctx: PipelineContext): Promise<void> {
     missingRel.push(rel);
     missingAbs.push(path.join(ctx.rootDir, rel));
   }
-  if (missingAbs.length === 0) return;
+
+  // Detect WASM-only files deleted from disk (#1073). The Rust orchestrator's
+  // `detect_removed_files` filter (#1070) skips files outside its supported
+  // extensions, so deletions of WASM-only languages don't reach the native
+  // purge path. JS doesn't notice either — the rest of this function only
+  // inserts rows. Result: stale `nodes`/`file_hashes` rows linger across
+  // incremental rebuilds until the next full rebuild.
+  const staleRel = computeWasmOnlyStaleFiles({
+    existingNodes,
+    existingHashes,
+    expected,
+    installedExts,
+    nativeSupported: NATIVE_SUPPORTED_EXTENSIONS,
+  });
+
+  if (missingAbs.length === 0 && staleRel.length === 0) return;
 
   // Now that we know there's work to do, hand off to better-sqlite3 (needed
   // for the INSERT path below).
@@ -840,6 +909,29 @@ async function backfillNativeDroppedFiles(ctx: PipelineContext): Promise<void> {
     ctx.nativeFirstProxy = false;
   }
 
+  const dbConn = ctx.db as unknown as BetterSqlite3Database;
+
+  // Purge WASM-only files that were deleted from disk (#1073). Rust's
+  // detect_removed_files skips them and the insert path below never visits
+  // them, so without this their rows would persist across rebuilds until the
+  // next full rebuild reset the DB.
+  if (staleRel.length > 0) {
+    const { byReason: staleByReason, totals: staleTotals } = classifyNativeDrops(staleRel);
+    info(
+      `Detected ${staleRel.length} deleted WASM-only file(s) the native orchestrator skipped; purging stale rows: ${formatDropExtensionSummary(staleByReason['unsupported-by-native'])}`,
+    );
+    // staleRel is restricted above to extensions outside NATIVE_SUPPORTED_EXTENSIONS,
+    // so the native-extractor-failure bucket should always be empty here.
+    if (staleTotals['native-extractor-failure'] > 0) {
+      debug(
+        `backfillNativeDroppedFiles: stale-purge classified ${staleTotals['native-extractor-failure']} native-supported file(s) — unexpected; inspect the filter`,
+      );
+    }
+    purgeFilesData(dbConn, staleRel);
+  }
+
+  if (missingAbs.length === 0) return;
+
   // Classify drops so users see per-extension reasons instead of just a count
   // (#1011). `unsupported-by-native` is a legitimate parser limit (no Rust
   // extractor); `native-extractor-failure` indicates a real native bug since
@@ -888,7 +980,7 @@ async function backfillNativeDroppedFiles(ctx: PipelineContext): Promise<void> {
       exportKeys.push([exp.name, exp.kind, relPath, exp.line]);
     }
   }
-  const db = ctx.db as unknown as BetterSqlite3Database;
+  const db = dbConn;
   batchInsertNodes(db, rows);
 
   // Mark exported symbols in batches — mirrors insertDefinitionsAndExports.

tests/builder/wasm-only-stale-files.test.ts

@@ -0,0 +1,117 @@
+/**
+ * Unit tests for `computeWasmOnlyStaleFiles` (#1073).
+ *
+ * The Rust orchestrator's `detect_removed_files` filter (#1070) skips files
+ * outside its supported extensions, so deletions of WASM-only languages don't
+ * reach the native purge path. The JS-side backfill only inserts rows, so
+ * without this helper a deleted WASM-only file would leak `nodes`/`file_hashes`
+ * rows until the next full rebuild.
+ *
+ * These tests pass the extension sets as parameters so they remain meaningful
+ * even when every currently-registered language is natively supported
+ * (i.e. `installedExts == nativeSupported`). The bug surface re-opens any time
+ * a new WASM-only language enters the registry before its Rust extractor.
+ */
+import { describe, expect, it } from 'vitest';
+import { computeWasmOnlyStaleFiles } from '../../src/domain/graph/builder/pipeline.js';
+
+const NATIVE = new Set(['.ts', '.js', '.r']);
+const INSTALLED = new Set(['.ts', '.js', '.r', '.gleam', '.foo']);
+
+describe('computeWasmOnlyStaleFiles', () => {
+  it('returns WASM-only files present in DB but missing from disk', () => {
+    const stale = computeWasmOnlyStaleFiles({
+      existingNodes: new Set(['src/a.gleam', 'src/b.ts']),
+      existingHashes: new Set(['src/a.gleam', 'src/b.ts']),
+      expected: new Set(['src/b.ts']),
+      installedExts: INSTALLED,
+      nativeSupported: NATIVE,
+    });
+    expect(stale).toEqual(['src/a.gleam']);
+  });
+
+  it('skips natively-supported extensions — Rust owns their deletion path', () => {
+    const stale = computeWasmOnlyStaleFiles({
+      existingNodes: new Set(['src/old.ts', 'src/old.r']),
+      existingHashes: new Set(['src/old.ts', 'src/old.r']),
+      expected: new Set(),
+      installedExts: INSTALLED,
+      nativeSupported: NATIVE,
+    });
+    expect(stale).toEqual([]);
+  });
+
+  it('skips extensions with no installed WASM grammar', () => {
+    // .bar is not in installedExts — neither engine can parse it, so DB rows
+    // for it can't have been written by this codepath. Leave them alone.
+    const stale = computeWasmOnlyStaleFiles({
+      existingNodes: new Set(['src/x.bar']),
+      existingHashes: new Set(['src/x.bar']),
+      expected: new Set(),
+      installedExts: INSTALLED,
+      nativeSupported: NATIVE,
+    });
+    expect(stale).toEqual([]);
+  });
+
+  it('catches files that exist only in file_hashes (nodes missing)', () => {
+    // Legacy DB shape where file_hashes was written but `nodes` was not — the
+    // backfill should still recognise the file_hashes row as stale.
+    const stale = computeWasmOnlyStaleFiles({
+      existingNodes: new Set(),
+      existingHashes: new Set(['src/leftover.gleam']),
+      expected: new Set(),
+      installedExts: INSTALLED,
+      nativeSupported: NATIVE,
+    });
+    expect(stale).toEqual(['src/leftover.gleam']);
+  });
+
+  it('catches files that exist only in nodes (file_hashes missing)', () => {
+    const stale = computeWasmOnlyStaleFiles({
+      existingNodes: new Set(['src/leftover.gleam']),
+      existingHashes: new Set(),
+      expected: new Set(),
+      installedExts: INSTALLED,
+      nativeSupported: NATIVE,
+    });
+    expect(stale).toEqual(['src/leftover.gleam']);
+  });
+
+  it('deduplicates files appearing in both nodes and file_hashes', () => {
+    const stale = computeWasmOnlyStaleFiles({
+      existingNodes: new Set(['src/dup.gleam']),
+      existingHashes: new Set(['src/dup.gleam']),
+      expected: new Set(),
+      installedExts: INSTALLED,
+      nativeSupported: NATIVE,
+    });
+    expect(stale).toEqual(['src/dup.gleam']);
+  });
+
+  it('lowercases extensions to match registry/Rust normalisation', () => {
+    // R is conventionally written `.R` on disk. The registry and the Rust
+    // `LanguageKind::from_extension` accept both cases; `installedExts` and
+    // `nativeSupported` carry the lowercase canonical form.
+    const stale = computeWasmOnlyStaleFiles({
+      existingNodes: new Set(['src/Plot.R']),
+      existingHashes: new Set(['src/Plot.R']),
+      expected: new Set(),
+      installedExts: INSTALLED,
+      nativeSupported: NATIVE,
+    });
+    // .R lowercases to .r which IS native-supported, so it should be skipped.
+    expect(stale).toEqual([]);
+  });
+
+  it('returns empty when DB and disk agree', () => {
+    const stale = computeWasmOnlyStaleFiles({
+      existingNodes: new Set(['src/a.gleam', 'src/b.ts']),
+      existingHashes: new Set(['src/a.gleam', 'src/b.ts']),
+      expected: new Set(['src/a.gleam', 'src/b.ts']),
+      installedExts: INSTALLED,
+      nativeSupported: NATIVE,
+    });
+    expect(stale).toEqual([]);
+  });
+});