fix: correctly leave only staged files for running tasks

lib/gitWorkflow.js

@@ -68,19 +68,18 @@ class GitWorkflow {
       debug('Done backing up merge state!')
     }
 
-    // Get stash of entire original state, including unstaged changes
+    // Get diff of staged modifications. This will be applied back to the index. after stashing all changes.
+    // The `git stash save --keep-index` option cannot be used since it resurrects deleted files on
+    // git versions before v2.23.0 (https://github.com/git/git/blob/master/Documentation/RelNotes/2.23.0.txt#L322)
+    const stagedDiff = await this.execGit(['diff', '--cached'])
+
+    // Save stash of entire original state, including unstaged and untracked changes.
+    // This should remove all changes from the index.
     await this.execGit(['stash', 'save', '--quiet', '--include-untracked', STASH])
-    // Apply index from previous stash back to enable running tasks against
-    // staged files only. `git stash --keep-index` cannot be used here because of
-    // a bug affecting deleted files. The bug has been fixed in git v2.23.0
-    // See https://github.com/git/git/blob/master/Documentation/RelNotes/2.23.0.txt#L322
-    await this.execGit(['stash', 'apply', '--index', await this.getBackupStash()])
-    // Clear any unstaged changes since they are saved in the stash,
-    // and shouldn't be affected by tasks
-    await this.execGit(['clean', '-df'])
-    await this.execGit(['checkout', '.'])
-    // Since only staged files are now present, get a diff of unstaged changes
-    // by comparing current index against original stash, but in reverse
+
+    // Apply staged modifications back to the index
+    await this.execGit([...gitApplyArgs, '--index'], { input: `${stagedDiff}\n` })
+
     this.unstagedDiff = await this.execGit([
       'diff',
       '--unified=0',