Updating Recipe Fails When Project Located in Subfolder in Git Repository

src/Update/RecipePatcher.php

@@ -83,6 +83,8 @@ public function generatePatch(array $originalFiles, array $newFiles): RecipePatc
             }
         }
 
+        // Use git binary to get project path from repository root
+        $prefix = trim($this->execute('git rev-parse --show-prefix', $this->rootDir));
         $tmpPath = sys_get_temp_dir().'/_flex_recipe_update'.uniqid(mt_rand(), true);
         $this->filesystem->mkdir($tmpPath);
 
@@ -104,7 +106,7 @@ public function generatePatch(array $originalFiles, array $newFiles): RecipePatc
             $this->writeFiles($newFiles, $tmpPath);
             $this->execute('git add -A', $tmpPath);
 
-            $patchString = $this->execute('git diff --cached', $tmpPath);
+            $patchString = $this->execute(sprintf('git diff --cached --src-prefix "a/%s" --dst-prefix "b/%s"', $prefix, $prefix), $tmpPath);
             $removedPatches = [];
             $patchString = DiffHelper::removeFilesFromPatch($patchString, $deletedModifiedFiles, $removedPatches);
 
@@ -167,7 +169,7 @@ private function addMissingBlobs(array $blobs): array
     {
         $addedBlobs = [];
         foreach ($blobs as $hash => $contents) {
-            $blobPath = $this->rootDir.'/'.$this->getBlobPath($hash);
+            $blobPath = $this->getBlobPath($this->rootDir, $hash);
             if (file_exists($blobPath)) {
                 continue;
             }
@@ -192,18 +194,20 @@ private function generateBlobs(array $originalFiles, string $originalFilesRoot):
             }
 
             $hash = trim($this->execute('git hash-object '.ProcessExecutor::escape($filename), $originalFilesRoot));
-            $addedBlobs[$hash] = file_get_contents($originalFilesRoot.'/'.$this->getBlobPath($hash));
+            $addedBlobs[$hash] = file_get_contents($this->getBlobPath($originalFilesRoot, $hash));
         }
 
         return $addedBlobs;
     }
 
-    private function getBlobPath(string $hash): string
+    private function getBlobPath(string $gitRoot, string $hash): string
     {
+        $gitDir = trim($this->execute('git rev-parse --absolute-git-dir', $gitRoot));
+
         $hashStart = substr($hash, 0, 2);
         $hashEnd = substr($hash, 2);
 
-        return '.git/objects/'.$hashStart.'/'.$hashEnd;
+        return $gitDir.'/objects/'.$hashStart.'/'.$hashEnd;
     }
 
     private function _applyPatchFile(RecipePatch $patch)

tests/Update/RecipePatcherTest.php

@@ -233,9 +233,54 @@ public function testApplyPatch(array $filesCurrentlyInApp, RecipePatch $recipePa
         $this->assertSame($expectedConflicts, $hadConflicts);
     }
 
-    public function getApplyPatchTests(): iterable
+    /**
+     * @dataProvider getApplyPatchTests
+     */
+    public function testApplyPatchOnSubfolder(array $filesCurrentlyInApp, RecipePatch $recipePatch, array $expectedFiles, bool $expectedConflicts)
     {
-        $files = $this->getFilesForPatching();
+        $mainProjectPath = FLEX_TEST_DIR;
+        $subProjectPath = FLEX_TEST_DIR.'/ProjectA';
+
+        (new Process(['git', 'init'], $mainProjectPath))->mustRun();
+        (new Process(['git', 'config', 'user.name', 'Unit test'], $mainProjectPath))->mustRun();
+        (new Process(['git', 'config', 'user.email', ''], $mainProjectPath))->mustRun();
+
+        if (!file_exists($subProjectPath)) {
+            mkdir($subProjectPath, 0777, true);
+        }
+
+        foreach ($filesCurrentlyInApp as $file => $contents) {
+            $path = $subProjectPath.'/'.$file;
+            if (!file_exists(\dirname($path))) {
+                @mkdir(\dirname($path), 0777, true);
+            }
+            file_put_contents($path, $contents);
+        }
+        if (\count($filesCurrentlyInApp) > 0) {
+            (new Process(['git', 'add', '-A'], $subProjectPath))->mustRun();
+            (new Process(['git', 'commit', '-m', 'Committing original files'], $subProjectPath))->mustRun();
+        }
+
+        $patcher = new RecipePatcher($subProjectPath, $this->createMock(IOInterface::class));
+        $hadConflicts = !$patcher->applyPatch($recipePatch);
+
+        foreach ($expectedFiles as $file => $expectedContents) {
+            if (null === $expectedContents) {
+                $this->assertFileDoesNotExist($subProjectPath.'/'.$file);
+
+                continue;
+            }
+            $this->assertFileExists($subProjectPath.'/'.$file);
+            $this->assertSame($expectedContents, file_get_contents($subProjectPath.'/'.$file));
+        }
+
+        $this->assertSame($expectedConflicts, $hadConflicts);
+    }
+
+    public function getApplyPatchTests(string $testMethodName): iterable
+    {
+        $projectRootPath = ('testApplyPatchOnSubfolder' === $testMethodName) ? 'ProjectA/' : '';
+        $files = $this->getFilesForPatching($projectRootPath);
         $dotEnvClean = $files['dot_env_clean'];
         $packageJsonConflict = $files['package_json_conflict'];
         $webpackEncoreAdded = $files['webpack_encore_added'];
@@ -393,7 +438,7 @@ public function getIntegrationTests(): iterable
      *      * original_recipe
      *      * updated_recipe.
      */
-    private function getFilesForPatching(): array
+    private function getFilesForPatching(string $projectPath = ''): array
     {
         $files = [
             // .env
@@ -538,7 +583,7 @@ private function getFilesForPatching(): array
         foreach ($files as $key => $data) {
             $files[$key] = array_merge(
                 $data,
-                $this->generatePatchData($data['filename'], $data['original_recipe'], $data['updated_recipe'])
+                $this->generatePatchData($projectPath.$data['filename'], $data['original_recipe'], $data['updated_recipe'])
             );
         }