diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index d65a74e3..054bd341 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -3,8 +3,9 @@ name: CI
 on:
   push:
     branches: [main]
+  # Every pull request, whatever its base: stacked PRs need their checks
+  # before the branch under them merges.
   pull_request:
-    branches: [main]
 
 # Cancel superseded PR runs, but never group `push` events together — otherwise
 # back-to-back merges to main could silently drop intermediate CI runs even
diff --git a/scripts/patch-nativephp.php b/scripts/patch-nativephp.php
index 0d091386..f7fa4c4a 100644
--- a/scripts/patch-nativephp.php
+++ b/scripts/patch-nativephp.php
@@ -1969,38 +1969,54 @@ function rfaNativePhpPatchSet(): array
     ];
 }
 
+/**
+ * Every edit the set makes carries a `[rfa <name>]` comment, so a target
+ * holding this text was written by some revision of this script.
+ */
+const RFA_PATCH_MARKER = '[rfa ';
+
 /**
  * Apply the whole patch set under `$distRoot`, or none of it.
  *
+ * Patches are always applied to the stock file, never to the output of an
+ * earlier revision of this script. The first run over a vendor tree copies
+ * each target into `$stockRoot` before rewriting it; every later run patches
+ * that copy and writes the result over whatever the target holds, so editing
+ * a patch needs no upgrade path from its previous output. A target that
+ * carries rfa edits but has no stock copy comes from a script revision that
+ * kept none, and is refused with a reinstall hint rather than guessed at.
+ *
  * Three phases, in order:
  *
- *  1. **Preflight.** Read each target once and run its edits in memory. A file
- *     that is missing entirely is reported as absent and skipped — the release
- *     build re-runs this hook over a pruned `--no-dev` copy where the plugin
- *     dist legitimately isn't there. A file that is present but whose expected
- *     shape is gone blocks the run.
+ *  1. **Preflight.** Read each target once, pick its stock text, and run the
+ *     edits in memory. A file that is missing entirely is reported as absent
+ *     and skipped — the release build re-runs this hook over a pruned
+ *     `--no-dev` copy where the plugin dist legitimately isn't there. A file
+ *     that is present but whose expected shape is gone blocks the run.
  *  2. **Abort on any block.** Nothing has been written yet, so there is nothing
  *     to undo.
- *  3. **Write.** Each changed file goes to a sibling temporary file that is
- *     renamed into place, so a reader never sees a half-written file. If a
- *     later write fails, the files already renamed are restored from the
+ *  3. **Write.** A missing or outdated stock copy is stored first. Each
+ *     changed target then goes to a sibling temporary file that is renamed
+ *     into place, so a reader never sees a half-written file. If a later
+ *     write fails, the targets already renamed are restored from the
  *     originals held in memory.
  *
- * @return array{applied: list<string>, unchanged: list<string>, blocked: list<string>, absent: list<string>, written: list<string>, error: ?string, rolledBack: bool}
+ * @return array{applied: list<string>, unchanged: list<string>, blocked: list<string>, stale: list<string>, absent: list<string>, written: list<string>, error: ?string, rolledBack: bool}
  */
-function applyRfaNativePhpPatchSet(string $distRoot): array
+function applyRfaNativePhpPatchSet(string $distRoot, string $stockRoot): array
 {
     $result = [
         'applied' => [],
         'unchanged' => [],
         'blocked' => [],
+        'stale' => [],
         'absent' => [],
         'written' => [],
         'error' => null,
         'rolledBack' => false,
     ];
 
-    /** @var array<string, array{original: string, patched: string}> $files */
+    /** @var array<string, array{live: string, patched: string, stockPath: string, storeStock: bool, changed: list<string>, unchanged: list<string>}> $files */
     $files = [];
 
     foreach (rfaNativePhpPatchSet() as $patch) {
@@ -2013,15 +2029,36 @@ function applyRfaNativePhpPatchSet(string $distRoot): array
                 continue;
             }
 
-            $original = @file_get_contents($path);
+            $live = @file_get_contents($path);
+
+            if ($live === false) {
+                $result['blocked'][] = $patch['name'];
+
+                continue;
+            }
+
+            // A target without rfa edits is stock, and becomes the stock copy
+            // when the stored one is missing or differs (a reinstalled or
+            // upgraded plugin). A patched target starts from its stored copy.
+            $stockPath = $stockRoot.'/'.rfaStockKey($patch['file']);
+            $stored = is_file($stockPath) ? @file_get_contents($stockPath) : false;
+            $isPatched = str_contains($live, RFA_PATCH_MARKER);
 
-            if ($original === false) {
+            if ($isPatched && $stored === false) {
                 $result['blocked'][] = $patch['name'];
+                $result['stale'][] = $patch['name'];
 
                 continue;
             }
 
-            $files[$path] = ['original' => $original, 'patched' => $original];
+            $files[$path] = [
+                'live' => $live,
+                'patched' => $isPatched ? $stored : $live,
+                'stockPath' => $stockPath,
+                'storeStock' => ! $isPatched && $stored !== $live,
+                'changed' => [],
+                'unchanged' => [],
+            ];
         }
 
         $next = $patch['apply']($files[$path]['patched']);
@@ -2032,7 +2069,7 @@ function applyRfaNativePhpPatchSet(string $distRoot): array
             continue;
         }
 
-        $result[$next === $files[$path]['patched'] ? 'unchanged' : 'applied'][] = $patch['name'];
+        $files[$path][$next === $files[$path]['patched'] ? 'unchanged' : 'changed'][] = $patch['name'];
         $files[$path]['patched'] = $next;
     }
 
@@ -2053,7 +2090,23 @@ function applyRfaNativePhpPatchSet(string $distRoot): array
     $renamed = [];
 
     foreach ($files as $path => $contents) {
-        if ($contents['patched'] === $contents['original']) {
+        // A target already holding this revision's output reports every patch
+        // as unchanged, whatever the in-memory run from stock had to do.
+        if ($contents['patched'] === $contents['live']) {
+            $result['unchanged'] = [...$result['unchanged'], ...$contents['changed'], ...$contents['unchanged']];
+        } else {
+            $result['applied'] = [...$result['applied'], ...$contents['changed']];
+            $result['unchanged'] = [...$result['unchanged'], ...$contents['unchanged']];
+        }
+
+        if ($contents['storeStock'] && ! rfaStoreStockCopy($contents['stockPath'], $contents['live'])) {
+            $result['error'] = $contents['stockPath'];
+            $result['rolledBack'] = rfaRestoreFiles($renamed);
+
+            return $result;
+        }
+
+        if ($contents['patched'] === $contents['live']) {
             continue;
         }
 
@@ -2064,13 +2117,48 @@ function applyRfaNativePhpPatchSet(string $distRoot): array
             return $result;
         }
 
-        $renamed[$path] = $contents['original'];
+        $renamed[$path] = $contents['live'];
         $result['written'][] = $path;
     }
 
     return $result;
 }
 
+/**
+ * Where a target's stock copy lives under the stock root: its path relative
+ * to the vendored `resources/electron` directory, with `..` folded away.
+ */
+function rfaStockKey(string $file): string
+{
+    $segments = [];
+
+    foreach (explode('/', 'electron-plugin/dist/'.$file) as $segment) {
+        if ($segment === '..') {
+            array_pop($segments);
+
+            continue;
+        }
+
+        if ($segment !== '' && $segment !== '.') {
+            $segments[] = $segment;
+        }
+    }
+
+    return implode('/', $segments);
+}
+
+/**
+ * Store the stock text of a target, creating the directory it lives in.
+ */
+function rfaStoreStockCopy(string $stockPath, string $contents): bool
+{
+    if (! is_dir(dirname($stockPath)) && ! @mkdir(dirname($stockPath), 0755, true) && ! is_dir(dirname($stockPath))) {
+        return false;
+    }
+
+    return rfaWriteFileAtomically($stockPath, $contents);
+}
+
 /**
  * Replace `$path` with `$contents` through a sibling temporary file, so the
  * file is either its old self or its new self and never a truncated mix.
@@ -2127,9 +2215,19 @@ function rfaNativePhpDistRoot(): string
     return dirname(__DIR__).'/vendor/nativephp/desktop/resources/electron/electron-plugin/dist';
 }
 
+/**
+ * Where the stock copies of the patched files are kept: inside the vendored
+ * package, so Composer drops them with the package, and outside its
+ * `resources/electron` tree, which the build copies whole.
+ */
+function rfaNativePhpStockRoot(): string
+{
+    return dirname(__DIR__).'/vendor/nativephp/desktop/.rfa-stock';
+}
+
 // Run when executed directly (not when required by tests)
 if (realpath($_SERVER['SCRIPT_FILENAME'] ?? '') === realpath(__FILE__)) {
-    $outcome = applyRfaNativePhpPatchSet(rfaNativePhpDistRoot());
+    $outcome = applyRfaNativePhpPatchSet(rfaNativePhpDistRoot(), rfaNativePhpStockRoot());
 
     /** @var array<string, string> $summaries */
     $summaries = array_column(rfaNativePhpPatchSet(), 'summary', 'name');
@@ -2143,6 +2241,16 @@ function rfaNativePhpDistRoot(): string
     }
 
     foreach ($outcome['blocked'] as $name) {
+        if (in_array($name, $outcome['stale'], true)) {
+            fwrite(STDERR, sprintf(
+                "  ERROR: the '%s' patch (%s) targets a file already patched by an earlier revision of this script that kept no stock copy, so NOTHING was patched. Reinstall the plugin to start from stock: rm -rf vendor/nativephp/desktop && composer install\n",
+                $name,
+                $summaries[$name],
+            ));
+
+            continue;
+        }
+
         fwrite(STDERR, sprintf(
             "  ERROR: the '%s' patch (%s) could not be applied, so NOTHING was patched. The vendored NativePHP files changed shape or are incomplete — update scripts/patch-nativephp.php to match them, or reinstall nativephp/desktop.\n",
             $name,
diff --git a/tests/Unit/Scripts/NativePhpPatchSetTest.php b/tests/Unit/Scripts/NativePhpPatchSetTest.php
index e7728e1a..bc18b88d 100644
--- a/tests/Unit/Scripts/NativePhpPatchSetTest.php
+++ b/tests/Unit/Scripts/NativePhpPatchSetTest.php
@@ -1,5 +1,6 @@
 <?php
 
+use Illuminate\Support\Facades\File;
 use Symfony\Component\Process\Process;
 use Tests\Helpers\InteractsWithTestRepositories;
 use Tests\TestCase;
@@ -36,6 +37,22 @@ function stubDistRoot(string $root, ?callable $mutate = null): string
     return $root;
 }
 
+/**
+ * Run the set the way the composer hook does, keeping the stock copies beside
+ * the throwaway tree rather than in the real vendor directory.
+ *
+ * @return array{applied: list<string>, unchanged: list<string>, blocked: list<string>, stale: list<string>, absent: list<string>, written: list<string>, error: ?string, rolledBack: bool}
+ */
+function applyPatchSet(string $root): array
+{
+    return applyRfaNativePhpPatchSet($root, stockRootFor($root));
+}
+
+function stockRootFor(string $root): string
+{
+    return dirname($root, 2).'/.rfa-stock';
+}
+
 /** @return array<string, string> */
 function distSnapshot(string $root): array
 {
@@ -57,12 +74,20 @@ function distSnapshot(string $root): array
         ->toEndWith('/vendor/nativephp/desktop/resources/electron/electron-plugin/dist');
 });
 
+test('the stock copies live in the vendored package but outside the copied electron tree', function () {
+    expect(rfaNativePhpStockRoot())
+        ->toEndWith('/vendor/nativephp/desktop/.rfa-stock')
+        ->and(rfaStockKey('server/php.js'))->toBe('electron-plugin/dist/server/php.js')
+        ->and(rfaStockKey('../../src/main/index.js'))->toBe('src/main/index.js')
+        ->and(rfaStockKey('../../electron-builder.mjs'))->toBe('electron-builder.mjs');
+});
+
 // -- Applying the whole set --
 
 test('applies every patch in one run', function () {
     $root = stubDistRoot($this->createTempDirectory('rfa_test_dist_'));
 
-    $outcome = applyRfaNativePhpPatchSet($root);
+    $outcome = applyPatchSet($root);
 
     expect($outcome['applied'])->toBe(['preload-file-bridge', 'preload-renderer-ready', 'window-theme', 'renderer-ready-window', 'launch-timeline-window', 'server-optimize', 'server-workers', 'launch-timeline-server', 'cookie-after-ready', 'preflight-cache', 'splash-window', 'resolved-appearance', 'early-php-boot', 'launch-timeline', 'php-extraction', 'php-build-wait'])
         ->and($outcome['blocked'])->toBeEmpty()
@@ -119,7 +144,7 @@ function distSnapshot(string $root): array
 test('a remembered maximize stays transparent until the settled frame is presented', function () {
     $root = stubDistRoot($this->createTempDirectory('rfa_test_dist_'));
 
-    applyRfaNativePhpPatchSet($root);
+    applyPatchSet($root);
 
     expect(file_get_contents($root.'/server/api/window.js'))
         ->toContain("opacity: id === 'main' ? 0 : 1")
@@ -136,7 +161,7 @@ function distSnapshot(string $root): array
     // each edit based on the output of the previous edit.
     $root = stubDistRoot($this->createTempDirectory('rfa_test_dist_'));
 
-    applyRfaNativePhpPatchSet($root);
+    applyPatchSet($root);
 
     $index = file_get_contents($root.'/index.js');
 
@@ -156,10 +181,10 @@ function distSnapshot(string $root): array
 test('a second run changes nothing', function () {
     $root = stubDistRoot($this->createTempDirectory('rfa_test_dist_'));
 
-    applyRfaNativePhpPatchSet($root);
+    applyPatchSet($root);
     $afterFirst = distSnapshot($root);
 
-    $outcome = applyRfaNativePhpPatchSet($root);
+    $outcome = applyPatchSet($root);
 
     expect($outcome['applied'])->toBeEmpty()
         ->and($outcome['unchanged'])->toHaveCount(16)
@@ -167,6 +192,99 @@ function distSnapshot(string $root): array
         ->and(distSnapshot($root))->toBe($afterFirst);
 });
 
+// -- Patching from the stock copy --
+
+test('every patched target carries the marker the stock check looks for', function () {
+    $root = stubDistRoot($this->createTempDirectory('rfa_test_dist_'));
+
+    applyPatchSet($root);
+
+    foreach (distSnapshot($root) as $file => $contents) {
+        expect($contents)->toContain(RFA_PATCH_MARKER);
+    }
+});
+
+test('the first run stores a stock copy of every target', function () {
+    $root = stubDistRoot($this->createTempDirectory('rfa_test_dist_'));
+    $stock = distSnapshot($root);
+
+    applyPatchSet($root);
+
+    foreach ($stock as $file => $contents) {
+        expect(file_get_contents(stockRootFor($root).'/'.rfaStockKey($file)))->toBe($contents, $file);
+    }
+});
+
+test('a tree patched by an earlier revision is re-patched from the stock copy', function () {
+    // Simulate an older script revision: its output carries rfa edits but not
+    // this revision's text. No patch anchors on such a file, so the run must
+    // start over from the stock copy rather than upgrade in place.
+    $root = stubDistRoot($this->createTempDirectory('rfa_test_dist_'));
+
+    applyPatchSet($root);
+    $fresh = distSnapshot($root);
+
+    file_put_contents($root.'/server/php.js', str_replace('rfaNeedsFullOptimize', 'rfaNeedsOptimize', $fresh['server/php.js']));
+    file_put_contents($root.'/index.js', "// [rfa patch] an earlier revision\n".stockIndexForSplash()."\n".stockIndex());
+
+    $outcome = applyPatchSet($root);
+
+    expect($outcome['blocked'])->toBeEmpty()
+        ->and($outcome['applied'])->toBe(collect(rfaNativePhpPatchSet())->whereIn('file', ['server/php.js', 'index.js'])->pluck('name')->all())
+        ->and($outcome['written'])->toBe([$root.'/server/php.js', $root.'/index.js'])
+        ->and(distSnapshot($root))->toBe($fresh);
+});
+
+test('a patched tree without a stock copy is refused with a reinstall hint', function () {
+    $root = stubDistRoot($this->createTempDirectory('rfa_test_dist_'));
+
+    applyPatchSet($root);
+    $before = distSnapshot($root);
+    File::deleteDirectory(stockRootFor($root));
+
+    $outcome = applyPatchSet($root);
+
+    expect($outcome['stale'])->toBe(collect(rfaNativePhpPatchSet())->pluck('name')->all())
+        ->and($outcome['blocked'])->toBe($outcome['stale'])
+        ->and($outcome['written'])->toBeEmpty()
+        ->and(distSnapshot($root))->toBe($before);
+});
+
+test('a reinstalled plugin replaces the stock copy and is patched from the new text', function () {
+    $root = stubDistRoot($this->createTempDirectory('rfa_test_dist_'));
+
+    applyPatchSet($root);
+
+    $reinstalled = "// a newer plugin release\n".stockUtils();
+    file_put_contents($root.'/server/utils.js', $reinstalled);
+
+    $outcome = applyPatchSet($root);
+
+    expect($outcome['applied'])->toBe(collect(rfaNativePhpPatchSet())->where('file', 'server/utils.js')->pluck('name')->all())
+        ->and(file_get_contents(stockRootFor($root).'/electron-plugin/dist/server/utils.js'))->toBe($reinstalled)
+        ->and(file_get_contents($root.'/server/utils.js'))->toStartWith('// a newer plugin release')
+        ->and(file_get_contents($root.'/server/utils.js'))->toContain('[rfa cookie after ready]');
+});
+
+test('the composer hook names the reinstall command for a stale tree', function () {
+    $root = stubDistRoot($this->createTempDirectory('rfa_test_dist_'));
+
+    applyPatchSet($root);
+    File::deleteDirectory(stockRootFor($root));
+
+    $process = new Process(
+        ['php', '-r', sprintf(
+            'require %s; $o = applyRfaNativePhpPatchSet(%s, %s); exit($o["blocked"] === [] && $o["error"] === null ? 0 : 1);',
+            var_export(dirname(__DIR__, 3).'/scripts/patch-nativephp.php', true),
+            var_export($root, true),
+            var_export(stockRootFor($root), true),
+        )],
+    );
+    $process->run();
+
+    expect($process->getExitCode())->toBe(1);
+});
+
 // -- Preflight: one missing block stops the whole set --
 
 test('one reshaped source block leaves every file untouched', function () {
@@ -182,7 +300,7 @@ function distSnapshot(string $root): array
     });
     $before = distSnapshot($root);
 
-    $outcome = applyRfaNativePhpPatchSet($root);
+    $outcome = applyPatchSet($root);
 
     expect($outcome['blocked'])->toBe(['splash-window', 'resolved-appearance', 'early-php-boot'])
         ->and($outcome['written'])->toBeEmpty()
@@ -195,7 +313,7 @@ function distSnapshot(string $root): array
     });
     $before = distSnapshot($root);
 
-    $outcome = applyRfaNativePhpPatchSet($root);
+    $outcome = applyPatchSet($root);
 
     expect($outcome['blocked'])->toBe(['server-optimize', 'server-workers', 'launch-timeline-server'])
         ->and(distSnapshot($root))->toBe($before);
@@ -209,7 +327,7 @@ function distSnapshot(string $root): array
 
     chmod($root.'/server/php.js', 0000);
 
-    $outcome = applyRfaNativePhpPatchSet($root);
+    $outcome = applyPatchSet($root);
 
     chmod($root.'/server/php.js', 0644);
 
@@ -227,7 +345,7 @@ function distSnapshot(string $root): array
     $root = stubDistRoot($this->createTempDirectory('rfa_test_dist_'), fn (string $root) => chmod($root, 0555));
     $before = distSnapshot($root);
 
-    $outcome = applyRfaNativePhpPatchSet($root);
+    $outcome = applyPatchSet($root);
 
     chmod($root, 0755);
 
@@ -240,7 +358,7 @@ function distSnapshot(string $root): array
 test('a run leaves no temporary files behind', function () {
     $root = stubDistRoot($this->createTempDirectory('rfa_test_dist_'));
 
-    applyRfaNativePhpPatchSet($root);
+    applyPatchSet($root);
 
     expect(glob($root.'/*.rfa-patch-*'))->toBeEmpty()
         ->and(glob($root.'/*/*.rfa-patch-*'))->toBeEmpty();
@@ -249,7 +367,7 @@ function distSnapshot(string $root): array
 test('a rewritten file keeps its original permissions', function () {
     $root = stubDistRoot($this->createTempDirectory('rfa_test_dist_'), fn (string $root) => chmod($root.'/server/php.js', 0640));
 
-    applyRfaNativePhpPatchSet($root);
+    applyPatchSet($root);
 
     expect(fileperms($root.'/server/php.js') & 0777)->toBe(0640);
 });
@@ -259,7 +377,7 @@ function distSnapshot(string $root): array
 test('an absent dist tree is reported, not failed', function () {
     // The release build re-runs the hook via `composer install --no-dev` on a
     // pruned copy where the plugin dist is not present.
-    $outcome = applyRfaNativePhpPatchSet(sys_get_temp_dir().'/rfa_test_dist_nowhere_'.getmypid());
+    $outcome = applyPatchSet(sys_get_temp_dir().'/rfa_test_dist_nowhere_'.getmypid().'/electron-plugin/dist');
 
     expect($outcome['absent'])->toHaveCount(16)
         ->and($outcome['blocked'])->toBeEmpty()
@@ -273,9 +391,10 @@ function distSnapshot(string $root): array
 
     $process = new Process(
         ['php', '-r', sprintf(
-            'require %s; $o = applyRfaNativePhpPatchSet(%s); exit($o["blocked"] === [] && $o["error"] === null ? 0 : 1);',
+            'require %s; $o = applyRfaNativePhpPatchSet(%s, %s); exit($o["blocked"] === [] && $o["error"] === null ? 0 : 1);',
             var_export(dirname(__DIR__, 3).'/scripts/patch-nativephp.php', true),
             var_export($root, true),
+            var_export(stockRootFor($root), true),
         )],
     );
     $process->run();
@@ -288,9 +407,10 @@ function distSnapshot(string $root): array
 
     $process = new Process(
         ['php', '-r', sprintf(
-            'require %s; $o = applyRfaNativePhpPatchSet(%s); exit($o["blocked"] === [] && $o["error"] === null ? 0 : 1);',
+            'require %s; $o = applyRfaNativePhpPatchSet(%s, %s); exit($o["blocked"] === [] && $o["error"] === null ? 0 : 1);',
             var_export(dirname(__DIR__, 3).'/scripts/patch-nativephp.php', true),
             var_export($root, true),
+            var_export(stockRootFor($root), true),
         )],
     );
     $process->run();
@@ -337,7 +457,7 @@ function distSnapshot(string $root): array
     $root = stubDistRoot($this->createTempDirectory('rfa_test_dist_'), fn (string $root) => unlink($root.'/server/php.js'));
     $before = distSnapshot($root);
 
-    $outcome = applyRfaNativePhpPatchSet($root);
+    $outcome = applyPatchSet($root);
 
     expect($outcome['absent'])->toBe(['server-optimize', 'server-workers', 'launch-timeline-server'])
         ->and($outcome['blocked'])->toBe(['server-optimize', 'server-workers', 'launch-timeline-server'])