Vfs fix 2

builtin/checkout.c

@@ -641,6 +641,13 @@ static int checkout_paths(const struct checkout_opts *opts,
 		checkout_index = opts->checkout_index;
 
 	if (checkout_index) {
+		/* Some scenarios that checkout the index may update skipworktree bits,
+		 * such as `restore --staged` after `cherry-pick -n` or `reset --soft`,
+		 * so this flag should be set to ensure the correct virtual filesystem
+		 * event is sent.
+		 */
+		the_repository->index->updated_skipworktree = 1;
+
 		if (write_locked_index(the_repository->index, &lock_file, COMMIT_LOCK))
 			die(_("unable to write new index file"));
 	} else {

read-cache-ll.h

@@ -176,7 +176,8 @@
 		 drop_cache_tree : 1,
 		 updated_workdir : 1,
 		 updated_skipworktree : 1,
-		 fsmonitor_has_run_once : 1;
+		 fsmonitor_has_run_once : 1,
+		 clear_skip_worktree_for_added_entries : 0;
 	enum sparse_index_mode sparse_index;
 	struct hashmap name_hash;
 	struct hashmap dir_hash;

sequencer.c

@@ -753,6 +753,7 @@ static int do_recursive_merge(struct repository *r,
 	int clean, show_output;
 	int i;
 	struct lock_file index_lock = LOCK_INIT;
+	int flags;
 
 	if (repo_hold_locked_index(r, &index_lock, LOCK_REPORT_ON_ERROR) < 0)
 		return -1;
@@ -787,15 +788,26 @@ static int do_recursive_merge(struct repository *r,
 	 * to be replace with the tree the index matched before we
 	 * started doing any picks.
 	 */
+	if (opts->no_commit && core_virtualfilesystem) {
+		/* When using the virtual file system, staged new files
+		 * should clear SKIP_WORKTREE because the virtual file
+		 * system only tracks files that are not modified in index.
+		 * Without this, `restore --staged` will delete the new files
+		 * from disk as well as from index.
+		 */
+		o.repo->index->clear_skip_worktree_for_added_entries = 1;
+	}
 	merge_switch_to_result(&o, head_tree, &result, 1, show_output);
+	o.repo->index->clear_skip_worktree_for_added_entries = 0;
+
 	clean = result.clean;
 	if (clean < 0) {
 		rollback_lock_file(&index_lock);
 		return clean;
 	}
 
 	if (write_locked_index(r->index, &index_lock,
-			       COMMIT_LOCK | SKIP_IF_UNCHANGED))
+			       COMMIT_LOCK | SKIP_IF_UNCHANGED) < 0)
 		/*
 		 * TRANSLATORS: %s will be "revert", "cherry-pick" or
 		 * "rebase".

unpack-trees.c

@@ -1852,6 +1852,21 @@ static void mark_new_skip_worktree(struct pattern_list *pl,
 	enable_fscache(istate->cache_nr);
 	clear_ce_flags(istate, select_flag, skip_wt_flag, pl, show_progress);
 	disable_fscache();
+
+	/*
+	 * 3. If clear_skip_worktree_for_added_entries is set and we are checking for
+	 * added entries, clear skip_wt_flag from all added entries. 
+	 */
+	if ((select_flag & CE_ADDED)
+	    && istate->clear_skip_worktree_for_added_entries) {
+		for (i = 0; i < istate->cache_nr; i++) {
+			struct cache_entry *ce = istate->cache[i];
+			if ((ce->ce_flags & (CE_ADDED | skip_wt_flag))
+			    == (CE_ADDED | skip_wt_flag)) {
+				ce->ce_flags &= ~skip_wt_flag;
+			}
+		}
+	}
 }
 
 static void populate_from_existing_patterns(struct unpack_trees_options *o,