@@ -1982,6 +1982,103 @@ describe('main() — .spm-sync-watch-paths emission', () => {
   });
 });
 
+// ---------------------------------------------------------------------------
+// main() — libs/ symlinks for self-managed deps
+//
+// Xcode loads each libs/<SwiftName> symlink as a local package root. Replacing
+// one that did not change invalidates the package graph Xcode already holds,
+// and the build then fails with "Missing package product". So a sync that
+// changes nothing must leave every inode under libs/ — and libs/ itself —
+// untouched, while a dep that is gone must lose its symlink.
+// ---------------------------------------------------------------------------
+
+describe('main() — libs/ symlinks for self-managed deps', () => {
+  const {created} = useTempApps();
+
+  function buildApp(depNames) {
+    const appRoot = fs.realpathSync(
+      fs.mkdtempSync(path.join(os.tmpdir(), 'spm-libs-sync-')),
+    );
+    created.push(appRoot);
+    const rnRoot = path.join(appRoot, 'rn');
+    fs.mkdirSync(rnRoot, {recursive: true});
+    fs.writeFileSync(
+      path.join(appRoot, 'package.json'),
+      JSON.stringify({name: 'app'}),
+    );
+
+    const dependencies = {};
+    for (const npmName of depNames) {
+      // A hand-authored root Package.swift (no AUTOGEN marker) is what makes a
+      // dep self-managed.
+      const depDir = path.join(appRoot, 'node_modules', npmName);
+      fs.mkdirSync(depDir, {recursive: true});
+      fs.writeFileSync(
+        path.join(depDir, 'Package.swift'),
+        '// swift-tools-version:5.9\n// hand-authored\n',
+      );
+      fs.writeFileSync(path.join(depDir, 'Source.swift'), '// src\n');
+      dependencies[npmName] = {root: depDir, platforms: {ios: {}}};
+    }
+
+    const autolinkDir = path.join(appRoot, 'build', 'generated', 'autolinking');
+    fs.mkdirSync(autolinkDir, {recursive: true});
+    const writeAutolinkingJson = names =>
+      fs.writeFileSync(
+        path.join(autolinkDir, 'autolinking.json'),
+        JSON.stringify({
+          dependencies: Object.fromEntries(
+            names.map(n => [n, dependencies[n]]),
+          ),
+        }),
+      );
+    writeAutolinkingJson(depNames);
+
+    return {
+      libsDir: path.join(autolinkDir, 'libs'),
+      writeAutolinkingJson,
+      sync: () => main(['--app-root', appRoot, '--react-native-root', rnRoot]),
+    };
+  }
+
+  const inodesOf = libsDir =>
+    Object.fromEntries(
+      ['.', ...fs.readdirSync(libsDir)].map(entry => [
+        entry,
+        fs.lstatSync(path.join(libsDir, entry)).ino,
+      ]),
+    );
+
+  it('keeps every inode when nothing changed', () => {
+    const app = buildApp(['react-native-foo', 'react-native-bar']);
+
+    app.sync();
+    const before = inodesOf(app.libsDir);
+    expect(Object.keys(before).sort()).toEqual([
+      '.',
+      'ReactNativeBar',
+      'ReactNativeFoo',
+    ]);
+
+    app.sync();
+    expect(inodesOf(app.libsDir)).toEqual(before);
+  });
+
+  it('drops the symlink of a dep that is no longer autolinked', () => {
+    const app = buildApp(['react-native-foo', 'react-native-bar']);
+
+    app.sync();
+    expect(fs.readdirSync(app.libsDir).sort()).toEqual([
+      'ReactNativeBar',
+      'ReactNativeFoo',
+    ]);
+
+    app.writeAutolinkingJson(['react-native-foo']);
+    app.sync();
+    expect(fs.readdirSync(app.libsDir)).toEqual(['ReactNativeFoo']);
+  });
+});
+
 // ---------------------------------------------------------------------------
 // main() — the name a dep's podspec declares reaching a real manifest.
 // ---------------------------------------------------------------------------
 
@@ -234,6 +234,70 @@ describe('sync scripts', () => {
     );
   });
 
+  // Xcode writes per-user scheme state into <watched dir>/.swiftpm/ on every
+  // IDE build. Counting that as a change made every IDE build re-sync.
+  describe('the watched-directory staleness probe', () => {
+    // Runs the generated `find` in isolation, with $P/$STAMP bound as the
+    // build phase binds them.
+    function probe(watchedDir, stampFile) {
+      const findCommand = /\$\((find "\$P"[^()]*)\)/.exec(script)?.[1];
+      expect(findCommand).toBeDefined();
+      return execFileSync(
+        '/bin/bash',
+        [
+          '-c',
+          `set -euo pipefail\nP="$1"\nSTAMP="$2"\n${String(findCommand)}\n`,
+          'probe',
+          watchedDir,
+          stampFile,
+        ],
+        {encoding: 'utf8'},
+      );
+    }
+
+    let root;
+    let watchedDir;
+    let stampFile;
+    let schemeState;
+    let source;
+
+    beforeEach(() => {
+      root = fs.mkdtempSync(path.join(os.tmpdir(), 'spm-sync-stale-'));
+      watchedDir = path.join(root, 'node_modules', 'react-native-foo');
+      schemeState = path.join(
+        watchedDir,
+        '.swiftpm/xcode/xcuserdata/someone.xcuserdatad/xcschemes/xcschememanagement.plist',
+      );
+      source = path.join(watchedDir, 'Foo.swift');
+      fs.mkdirSync(path.dirname(schemeState), {recursive: true});
+      fs.writeFileSync(schemeState, '<plist/>\n');
+      fs.writeFileSync(source, '// src\n');
+      // The stamp is written after the tree, so nothing is newer until a test
+      // makes it so.
+      stampFile = path.join(root, '.spm-sync-stamp');
+      fs.writeFileSync(stampFile, '');
+    });
+
+    afterEach(() => {
+      fs.rmSync(root, {recursive: true, force: true});
+    });
+
+    const touch = file => {
+      const future = new Date(Date.now() + 10_000);
+      fs.utimesSync(file, future, future);
+    };
+
+    it('ignores Xcode-owned state under .swiftpm', () => {
+      touch(schemeState);
+      expect(probe(watchedDir, stampFile)).toBe('');
+    });
+
+    it('still reports a changed source file', () => {
+      touch(source);
+      expect(probe(watchedDir, stampFile).trim()).toBe(source);
+    });
+  });
+
   it('is deterministic, shared with the pre-action, and valid POSIX shell', () => {
     expect(buildSyncAutolinkingScript(baked)).toBe(script);
     expect(buildSchemePreActionScript(baked)).toBe(script);
 
@@ -1515,11 +1515,14 @@ function main(argv /*:: ?: Array<string> */) /*: void */ {
   // is the Swift module name (guaranteed unique per dep), so SPM's
   // path-basename-based package identity never collides — even when two
   // libs ship their own Package.swift inside `ios/` (a common convention).
-  // Wiped on every run; populated below as self-managed deps are visited.
+  // Populated below as self-managed deps are visited, then pruned. Entries
+  // that do not change keep their inode: Xcode holds each one as a loaded
+  // package root, and recreating one it already resolved fails the build with
+  // "Missing package product".
   const libsDir = path.join(outputDir, 'libs');
+  const wantedLibAliases /*: Set<string> */ = new Set();
   fs.mkdirSync(packagesDir, {recursive: true});
   fs.mkdirSync(headersDir, {recursive: true});
-  fs.rmSync(libsDir, {recursive: true, force: true});
   fs.mkdirSync(libsDir, {recursive: true});
 
   const wrapperDirs /*: Map<string, string> */ = new Map();
@@ -1652,6 +1655,7 @@ function main(argv /*:: ?: Array<string> */) /*: void */ {
       const realPackageDir = selfManagedDirs.get(target.name) ?? absSource;
       const aliasPath = path.join(libsDir, target.name);
       ensureSymlink(aliasPath, realPackageDir);
+      wantedLibAliases.add(target.name);
       aggregatorPackageDeps.push({
         swiftName: target.name,
         packagePath: `libs/${target.name}`,
@@ -1779,23 +1783,30 @@ function main(argv /*:: ?: Array<string> */) /*: void */ {
     });
   }
 
-  // Prune stale wrappers + header dirs for entries no longer autolinked.
-  // Preserve both wrapper-managed and self-managed names; only entries that
-  // are no longer autolinked at all get removed. Note: `packages/` only has
-  // wrapper-managed names (self-managed deps live in their own source dirs),
-  // but `headers/` has both since we populate the central tree for everyone.
+  // Prune stale wrappers, header dirs and lib aliases for entries no longer
+  // autolinked. Preserve both wrapper-managed and self-managed names; only
+  // entries that are no longer autolinked at all get removed. Note:
+  // `packages/` only has wrapper-managed names (self-managed deps live in
+  // their own source dirs), but `headers/` has both since we populate the
+  // central tree for everyone. `libs/` keeps only the aliases written above,
+  // so a dep that stopped being self-managed loses its alias too.
   const activeNames /*: Set<string> */ = new Set([
     ...wrapperDirs.keys(),
     ...selfManagedDirs.keys(),
   ]);
-  for (const subdir of ['packages', 'headers']) {
+  const pruneTargets /*: Array<[string, Set<string>]> */ = [
+    ['packages', activeNames],
+    ['headers', activeNames],
+    ['libs', wantedLibAliases],
+  ];
+  for (const [subdir, keptNames] of pruneTargets) {
     const dir = path.join(outputDir, subdir);
     try {
       const existing /*: Array<{name: string, isSymbolicLink(): boolean, isDirectory(): boolean}> */ =
         // $FlowFixMe[incompatible-type] Dirent typing
         fs.readdirSync(dir, {withFileTypes: true});
       for (const entry of existing) {
-        if (activeNames.has(entry.name)) continue;
+        if (keptNames.has(entry.name)) continue;
         const stale = path.join(dir, entry.name);
         if (entry.isSymbolicLink() || !entry.isDirectory()) {
           fs.unlinkSync(stale);
 
@@ -767,7 +767,9 @@ if [ "$STALE" -eq 0 ] && [ -f "$WATCH_FILE" ]; then
   while IFS= read -r P; do
     [ -z "$P" ] && continue
     if [ -d "$P" ]; then
-      if [ -n "$(find "$P" -newer "$STAMP" -print -quit 2>/dev/null)" ]; then
+      # .swiftpm holds Xcode's own per-user scheme state, which it rewrites
+      # during a build — reading it as a change makes every IDE build re-sync.
+      if [ -n "$(find "$P" -name .swiftpm -prune -o -newer "$STAMP" -print -quit 2>/dev/null)" ]; then
         STALE=1
         break
       fi