Comment important codepaths regarding nuking untracked files/dirs

In the last few commits we focused on code in unpack-trees.c that
mistakenly removed untracked files or directories.  There may be more of
those, but in this commit we change our focus: callers of toplevel
commands that are expected to remove untracked files or directories.

As noted previously, we have toplevel commands that are expected to
delete untracked files such as 'read-tree --reset', 'reset --hard', and
'checkout --force'.  However, that does not mean that other highlevel
commands that happen to call these other commands thought about or
conveyed to users the possibility that untracked files could be removed.
Audit the code for such callsites, and add comments near existing
callsites to mention whether these are safe or not.

My auditing is somewhat incomplete, though; it skipped several cases:
  * git-rebase--preserve-merges.sh: is in the process of being
    deprecated/removed, so I won't leave a note that there are
    likely more bugs in that script.
  * contrib/git-new-workdir: why is the -f flag being used in a new
    empty directory??  It shouldn't hurt, but it seems useless.
  * git-p4.py: Don't see why -f is needed for a new dir (maybe it's
    not and is just superfluous), but I'm not at all familiar with
    the p4 stuff
  * git-archimport.perl: Don't care; arch is long since dead
  * git-cvs*.perl: Don't care; cvs is long since dead

Also, the reset --hard in builtin/worktree.c looks safe, due to only
running in an empty directory.

Signed-off-by: Elijah Newren <newren@gmail.com>
Signed-off-by: Junio C Hamano <gitster@pobox.com>

builtin/stash.c

@@ -1521,6 +1521,7 @@ static int do_push_stash(const struct pathspec *ps, const char *stash_msg, int q
 		} else {
 			struct child_process cp = CHILD_PROCESS_INIT;
 			cp.git_cmd = 1;
+			/* BUG: this nukes untracked files in the way */
 			strvec_pushl(&cp.args, "reset", "--hard", "-q",
 				     "--no-recurse-submodules", NULL);
 			if (run_command(&cp)) {

builtin/submodule--helper.c

@@ -2864,6 +2864,10 @@ static int add_submodule(const struct add_data *add_data)
 		prepare_submodule_repo_env(&cp.env_array);
 		cp.git_cmd = 1;
 		cp.dir = add_data->sm_path;
+		/*
+		 * NOTE: we only get here if add_data->force is true, so
+		 * passing --force to checkout is reasonable.
+		 */
 		strvec_pushl(&cp.args, "checkout", "-f", "-q", NULL);
 
 		if (add_data->branch) {

contrib/rerere-train.sh

@@ -91,7 +91,7 @@ do
 		git checkout -q $commit -- .
 		git rerere
 	fi
-	git reset -q --hard
+	git reset -q --hard  # Might nuke untracked files...
 done
 
 if test -z "$branch"

submodule.c

@@ -1866,6 +1866,7 @@ static void submodule_reset_index(const char *path)
 
 	strvec_pushf(&cp.args, "--super-prefix=%s%s/",
 		     get_super_prefix_or_empty(), path);
+	/* TODO: determine if this might overwright untracked files */
 	strvec_pushl(&cp.args, "read-tree", "-u", "--reset", NULL);
 
 	strvec_push(&cp.args, empty_tree_oid_hex());