@@ -144,11 +144,18 @@ manifests. On the next build the phase re-syncs when a watched **file** is newer
 than the last sync, a watched **dir** has a newer child, or a watched path has
 **vanished** (a rename forces a re-sync so the config error surfaces).
 
+A watched path that does not exist yet is watched for **appearing**. When it is
+created, the next build re-syncs. So a plugin that builds precompiled modules
+should list their output folder, even when a fresh clone does not have it yet.
+List only folders that the Xcode build itself does not write to, or every build
+re-syncs.
+
 Unlike `flavoredFrameworks`, watch paths are best-effort: a non-array is ignored
 with a warning (never fatal), and each non-string / empty / **relative** entry
 is dropped with a warning. Absolute-only, because the generated phase tests
-these paths with no cwd context. The kept paths are folded into
-`<outputDir>/.spm-sync-watch-paths` alongside RN's own, then deduped and sorted.
+these paths with no cwd context. The kept paths are folded in with RN's own,
+deduped, and sorted: paths that exist go to `<outputDir>/.spm-sync-watch-paths`,
+and paths that do not exist yet go to `<outputDir>/.spm-sync-watch-absent`.
 
 ### `scriptPhases` — build-time shell phases on the app target
 
 
@@ -258,7 +258,7 @@ Because `deinit` drops the marker, it drops both.
 | Path                           | Written by                          | Contents                                                                                                                                                                                  |
 | ------------------------------ | ----------------------------------- | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
 | `build/generated/ios/`         | `add`, `update`, `sync`, `codegen`  | Codegen output plus the SwiftPM codegen manifest (the `React-GeneratedCode` package).                                                                                                     |
-| `build/generated/autolinking/` | `add`, `update`, `sync`             | `Package.swift`, `autolinking.json`, `packages/`, `libs/`, `headers/`, the `.spm-sync-stamp`, `.spm-sync-watch-paths`, and any `.spm-plugin-*.json` plugin manifests.                     |
+| `build/generated/autolinking/` | `add`, `update`, `sync`             | `Package.swift`, `autolinking.json`, `packages/`, `libs/`, `headers/`, the `.spm-sync-stamp`, `.spm-sync-watch-paths`, `.spm-sync-watch-absent`, and any `.spm-plugin-*.json` manifests.  |
 | `build/xcframeworks/`          | `add`, `update`, `sync`, `download` | The `debug/` and `release/` flavor slots (symlinks into the cache), `ReactHeadersTarget/`, the headers-only xcframeworks, `Package.swift`, `flavored-frameworks.json`, `.artifact-stamp`. |
 | `.build/`, `Package.resolved`  | Xcode / SwiftPM                     | SwiftPM's own build directory and resolution file. Machine-specific.                                                                                                                      |
 
@@ -711,6 +711,11 @@ _existing_ set of generated packages current; they do not create the first one.
      [plugin](./spm-autolinking-plugins.md#watchpaths--plugin-staleness-inputs)
      `watchPaths`; a watched file that is newer, a watched dir with a newer
      child, or a watched path that has **vanished** all mark stale
+   - every path in `.spm-sync-watch-absent` — watched paths that did not exist
+     at the last sync; one that **appears** marks stale. This includes each
+     dependency's root `Package.swift` and `.react-native/`: one that appears
+     later (e.g. after `spm scaffold`) changes self-managed detection. Projects
+     get this check after running `npx react-native spm update` once
 2. If any input is newer (or the stamp is missing): runs
    `npx react-native spm sync`, which re-executes autolinking + package
    generation (downloading artifacts if the cache slot is incomplete) and writes
 
@@ -1879,7 +1879,7 @@ describe('main() — scriptPhases sidecar', () => {
 // and deduped/sorted: (1) each module's source DIR; (2) each npm dep's
 // checked-in root Package.swift (FILE) and .react-native/ (DIR) — threaded from
 // the autolinking model's dep root, not derived by walking up; (3) plugin
-// watchPaths. Nonexistent paths are filtered at emission time.
+// watchPaths. Nonexistent paths go to .spm-sync-watch-absent instead.
 // ---------------------------------------------------------------------------
 
 describe('main() — .spm-sync-watch-paths emission', () => {
@@ -1920,8 +1920,8 @@ describe('main() — .spm-sync-watch-paths emission', () => {
     fs.writeFileSync(path.join(fooDir, 'Foo.swift'), '// src\n');
 
     // (C) A plugin-host dep contributing watchPaths: one existing absolute path
-    // (kept), one absent absolute path (filtered at emission), one relative
-    // path (dropped by invokePlugins).
+    // (kept), one absent absolute path (listed as absent), one relative path
+    // (dropped by invokePlugins).
     const expoDir = path.join(appRoot, 'node_modules', 'expo');
     fs.mkdirSync(path.join(expoDir, 'ios'), {recursive: true});
     fs.writeFileSync(path.join(expoDir, 'ios', 'Expo.mm'), '// native\n');
@@ -1940,14 +1940,22 @@ describe('main() — .spm-sync-watch-paths emission', () => {
         "    productDependencies: [{name: 'ExpoModulesCore', package: 'ExpoModulesCore'}],",
         '    watchPaths: [',
         "      path.join(__dirname, 'Package.swift'),", // exists → kept
-        "      path.join(__dirname, 'MISSING.swift'),", // absent → filtered at emission
+        "      path.join(__dirname, 'MISSING.swift'),", // absent → listed as absent
         "      'rel/manifest',", // relative → dropped by invokePlugins
         '    ],',
         '  };',
         '};',
       ].join('\n') + '\n',
     );
 
+    // (D) The app's project file: Xcode rewrites it on every IDE edit, so
+    // watching it would re-sync after each one.
+    fs.mkdirSync(path.join(appRoot, 'App.xcodeproj'));
+    fs.writeFileSync(
+      path.join(appRoot, 'App.xcodeproj', 'project.pbxproj'),
+      '\n',
+    );
+
     const autolinkDir = path.join(appRoot, 'build', 'generated', 'autolinking');
     fs.mkdirSync(autolinkDir, {recursive: true});
     fs.writeFileSync(
@@ -1972,13 +1980,64 @@ describe('main() — .spm-sync-watch-paths emission', () => {
     // (C) plugin's existing absolute watchPath is kept.
     expect(lines).toContain(path.join(expoDir, 'Package.swift'));
 
+    // (D) the app's project file is not watched.
+    expect(lines.some(l => l.includes('project.pbxproj'))).toBe(false);
+
     // Filtered / dropped entries never reach the file.
     expect(lines.some(l => l.includes('MISSING.swift'))).toBe(false);
     expect(lines.some(l => l.includes('rel/manifest'))).toBe(false);
 
     // Deduped and sorted (stable, deterministic output).
     expect(new Set(lines).size).toBe(lines.length);
     expect([...lines].sort()).toEqual(lines);
+
+    expect(
+      fs.readFileSync(path.join(autolinkDir, '.spm-sync-watch-absent'), 'utf8'),
+    ).toBe(path.join(expoDir, 'MISSING.swift') + '\n');
+  });
+
+  it('lists a dep root without Package.swift or .react-native/ as absent', () => {
+    const appRoot = fs.realpathSync(
+      fs.mkdtempSync(path.join(os.tmpdir(), 'spm-watch-absent-')),
+    );
+    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'}),
+    );
+
+    // Self-managed through ios/Package.swift, so nothing exists at the root.
+    const barDir = path.join(appRoot, 'node_modules', 'react-native-bar');
+    fs.mkdirSync(path.join(barDir, 'ios'), {recursive: true});
+    fs.writeFileSync(
+      path.join(barDir, 'ios', 'Package.swift'),
+      '// swift-tools-version:5.9\n// hand-authored\n',
+    );
+    fs.writeFileSync(path.join(barDir, 'ios', 'Bar.swift'), '// src\n');
+
+    const autolinkDir = path.join(appRoot, 'build', 'generated', 'autolinking');
+    fs.mkdirSync(autolinkDir, {recursive: true});
+    fs.writeFileSync(
+      path.join(autolinkDir, 'autolinking.json'),
+      JSON.stringify({
+        dependencies: {
+          'react-native-bar': {root: barDir, platforms: {ios: {}}},
+        },
+      }),
+    );
+
+    main(['--app-root', appRoot, '--react-native-root', rnRoot]);
+
+    expect(
+      fs.readFileSync(path.join(autolinkDir, '.spm-sync-watch-absent'), 'utf8'),
+    ).toBe(
+      [
+        path.join(barDir, '.react-native'),
+        path.join(barDir, 'Package.swift'),
+      ].join('\n') + '\n',
+    );
   });
 });
 
 
@@ -333,6 +333,42 @@ describe('sync scripts', () => {
     });
   });
 
+  it('re-syncs when a path listed as absent appears', () => {
+    const loop = /^ABSENT_FILE=[\s\S]*?^fi$/m.exec(script)?.[0];
+    expect(loop).toBeDefined();
+    const probe = srcRoot =>
+      execFileSync(
+        '/bin/bash',
+        [
+          '-c',
+          `set -euo pipefail\nSRCROOT="$1"\nSTALE=0\n${String(loop)}\necho "$STALE"\n`,
+          'probe',
+          srcRoot,
+        ],
+        {encoding: 'utf8'},
+      ).trim();
+
+    const root = fs.mkdtempSync(path.join(os.tmpdir(), 'spm-sync-absent-'));
+    try {
+      const autolinkDir = path.join(root, 'build/generated/autolinking');
+      fs.mkdirSync(autolinkDir, {recursive: true});
+      const watched = path.join(root, 'precompiled');
+      fs.mkdirSync(watched);
+      expect(probe(root)).toBe('0');
+
+      fs.writeFileSync(
+        path.join(autolinkDir, '.spm-sync-watch-absent'),
+        `${watched}\n`,
+      );
+      expect(probe(root)).toBe('1');
+
+      fs.rmdirSync(watched);
+      expect(probe(root)).toBe('0');
+    } finally {
+      fs.rmSync(root, {recursive: true, force: true});
+    }
+  });
+
   it('is deterministic, shared with the pre-action, and valid POSIX shell', () => {
     expect(buildSyncAutolinkingScript(baked)).toBe(script);
     expect(buildSchemePreActionScript(baked)).toBe(script);
 
@@ -65,7 +65,8 @@
  *         // Absolute paths (dirs OR files) the Xcode auto-sync build phase
  *         // should watch for staleness — e.g. the plugin dep's own
  *         // `Package.swift`, `expo-module.config.json`, and per-module
- *         // manifests. Folded into `.spm-sync-watch-paths`; a file edit or a
+ *         // manifests. Folded into `.spm-sync-watch-paths` (or
+ *         // `.spm-sync-watch-absent` while missing); a file edit or a
  *         // dir add/remove there re-triggers the sync. Relative/empty/non-string
  *         // entries are dropped with a warning; a non-array is ignored.
  *         watchPaths: ['/abs/path/Package.swift', '/abs/dir'],
 
@@ -1920,12 +1920,15 @@ function main(argv /*:: ?: Array<string> */) /*: void */ {
   //      stale until an unrelated install triggers a sync. The dep ROOT is
   //      threaded through the entry (entry.root, from the autolinking model),
   //      not derived by walking up from the (possibly nested) source dir.
+  //      Both are listed even when absent: one that appears later (e.g. after
+  //      `spm scaffold`) changes self-managed detection and needs a re-sync.
   //   3. Plugin-contributed paths (e.g. Expo's own Package.swift / per-module
   //      manifests) — already validated absolute in invokePlugins.
   // The phase distinguishes dir vs file with `-d`/`-f` at build time (no
-  // markers). The existsSync filter here is safe: these paths come from a
-  // successful sync so they exist now; a path that later VANISHES is caught at
-  // phase time against this file and forces a re-sync.
+  // markers). A listed path that later VANISHES forces a re-sync. Paths that do
+  // not exist yet go to .spm-sync-watch-absent, where one that APPEARS forces a
+  // re-sync; they stay out of this file because phases from older versions
+  // treat a missing listed path as stale.
   const watchCandidates /*: Array<string> */ = [...entryAbsDirs.values()];
   for (const entry of entries) {
     const root = entry.root;
@@ -1936,14 +1939,23 @@ function main(argv /*:: ?: Array<string> */) /*: void */ {
     watchCandidates.push(path.join(root, '.react-native'));
   }
   watchCandidates.push(...pluginWatchPaths);
-  const watchPaths = Array.from(new Set(watchCandidates))
-    .filter(p => p.length > 0 && fs.existsSync(p))
-    .sort();
+  const watchPaths /*: Array<string> */ = [];
+  const absentWatchPaths /*: Array<string> */ = [];
+  for (const p of Array.from(new Set(watchCandidates)).sort()) {
+    if (p.length > 0) {
+      (fs.existsSync(p) ? watchPaths : absentWatchPaths).push(p);
+    }
+  }
   fs.writeFileSync(
     path.join(outputDir, '.spm-sync-watch-paths'),
     watchPaths.join('\n') + (watchPaths.length > 0 ? '\n' : ''),
     'utf8',
   );
+  fs.writeFileSync(
+    path.join(outputDir, '.spm-sync-watch-absent'),
+    absentWatchPaths.join('\n') + (absentWatchPaths.length > 0 ? '\n' : ''),
+    'utf8',
+  );
 
   // AutolinkedAggregate is glue; needs at least one source file (Swift, so we
   // sidestep the Obj-C public-headers-dir requirement).
 
@@ -785,6 +785,19 @@ if [ "$STALE" -eq 0 ] && [ -f "$WATCH_FILE" ]; then
   done < "$WATCH_FILE"
 fi
 
+# Watched paths that did not exist at the last sync. One that APPEARS (e.g. a
+# plugin's precompiled output folder) forces a re-sync.
+ABSENT_FILE="$SRCROOT/build/generated/autolinking/.spm-sync-watch-absent"
+if [ "$STALE" -eq 0 ] && [ -f "$ABSENT_FILE" ]; then
+  while IFS= read -r P; do
+    [ -z "$P" ] && continue
+    if [ -e "$P" ]; then
+      STALE=1
+      break
+    fi
+  done < "$ABSENT_FILE"
+fi
+
 # Check 2: codegen spec files changed via git (covers monorepo after git pull)
 if [ "$STALE" -eq 0 ] && [ -f "$STAMP" ]; then
   STAMP_TIME=$(stat -f %m "$STAMP" 2>/dev/null || stat -c %Y "$STAMP" 2>/dev/null || echo 0)
 
@@ -324,7 +324,8 @@ export type PluginResult = {
   flavoredFrameworks: Array<PluginFlavoredFramework>,
   // Absolute paths (dirs or files) the Xcode auto-sync build phase should watch
   // for staleness, e.g. the plugin dep's own `Package.swift` and per-module
-  // manifests. Folded into `.spm-sync-watch-paths` by main().
+  // manifests. Folded into `.spm-sync-watch-paths` (or `.spm-sync-watch-absent`
+  // while missing) by main().
   watchPaths: Array<string>,
   // Build-time shell phases for the app target, recorded to
   // `.spm-plugin-script-phases.json` by main() and injected by `spm add`/