unpack-trees: check for missing submodule directory in merged_entry

Using `git checkout --recurse-submodules` to switch between a
branch with no submodules and a branch with initialized nested
submodules currently causes a fatal error:

    $ git checkout --recurse-submodules branch-with-nested-submodules
    fatal: exec '--super-prefix=submodule/nested/': cd to 'nested'
failed: No such file or directory
    error: Submodule 'nested' could not be updated.
    error: Submodule 'submodule/nested' cannot checkout new HEAD.
    error: Submodule 'submodule' could not be updated.
    M	submodule
    Switched to branch 'branch-with-nested-submodules'

The checkout succeeds but the worktree and index of the first level
submodule are left empty:

    $ cd submodule
    $ git -c status.submoduleSummary=1 status
    HEAD detached at b3ce885
    Changes to be committed:
      (use "git restore --staged <file>..." to unstage)
          deleted:    .gitmodules
          deleted:    first.t
          deleted:    nested

    fatal: not a git repository: 'nested/.git'
    Submodule changes to be committed:

    * nested 1e96f59...0000000:

    $ git ls-files -s
    $ # empty
    $ ls -A
    .git

The reason for the fatal error during the checkout is that a child git
process tries to cd into the yet unexisting nested submodule directory.
The sequence is the following:

1. The main git process (the one running in the superproject) eventually
reaches write_entry() in entry.c, which creates the first level
submodule directory and then calls submodule_move_head() in submodule.c,
which spawns `git read-tree` in the submodule directory.

2. The first child git process (the one in the submodule of the
superproject) eventually calls check_submodule_move_head() at
unpack_trees.c:2021, which calls submodule_move_head in dry-run mode,
which spawns `git read-tree` in the nested submodule directory.

3. The second child git process tries to chdir() in the yet unexisting
nested submodule directory in start_command() at run-command.c:829 and
dies before exec'ing.

The reason why check_submodule_move_head() is reached in the first child
and not in the main process is that it is inside an
if(submodule_from_ce()) construct, and submodule_from_ce() returns a
valid struct submodule pointer, whereas it returns a null pointer in the
main git process.

The reason why submodule_from_ce() returns a null pointer in the main
git process is because the call to cache_lookup_path() in config_from()
(called from submodule_from_path() in submodule_from_ce()) returns a
null pointer since the hashmap "for_path" in the submodule_cache of
the_repository is not yet populated. It is not populated because both
repo_get_oid(repo, GITMODULES_INDEX, &oid) and repo_get_oid(repo,
GITMODULES_HEAD, &oid) in config_from_gitmodules() at
submodule-config.c:639-640 return -1, as at this stage of the operation,
neither the HEAD of the superproject nor its index contain any
.gitmodules file.

In contrast, in the first child the hashmap is populated because
repo_get_oid(repo, GITMODULES_HEAD, &oid) returns 0 as the HEAD of the
first level submodule, i.e. .git/modules/submodule/HEAD, points to a
commit where .gitmodules is present and records 'nested' as a submodule.

Fix this bug by checking that the submodule directory exists before
calling check_submodule_move_head() in merged_entry() in the `if(!old)`
branch, i.e. if going from a commit with no submodule to a commit with a
submodule present.

Also protect the other call to check_submodule_move_head() in
merged_entry() the same way as it is safer, even though the `else if
(!(old->ce_flags & CE_CONFLICTED))` branch of the code is not at play in
the present bug.

The other calls to check_submodule_move_head() in other functions in
unpack_trees.c are all already protected by calls to lstat() somewhere
in
the program flow so we don't need additional protection for them.

All commands in the unpack_trees machinery are affected, i.e. checkout,
reset and read-tree when called with the --recurse-submodules flag.

This bug was first reported in [1].

[1]
https://lore.kernel.org/git/7437BB59-4605-48EC-B05E-E2BDB2D9DABC@gmail.com/

Reported-by: Philippe Blain <levraiphilippeblain@gmail.com>
Reported-by: Damien Robert <damien.olivier.robert@gmail.com>
Signed-off-by: Philippe Blain <levraiphilippeblain@gmail.com>
Signed-off-by: Junio C Hamano <gitster@pobox.com>

t/lib-submodule-update.sh

@@ -626,6 +626,7 @@ test_submodule_forced_switch () {
 # New test cases
 # - Removing a submodule with a git directory absorbs the submodules
 #   git directory first into the superproject.
+# - Switching from no submodule to nested submodules
 
 # Internal function; use test_submodule_switch_recursing_with_args() or
 # test_submodule_forced_switch_recursing_with_args() instead.
@@ -683,6 +684,19 @@ test_submodule_recursing_with_args_common() {
 			test_submodule_content sub1 origin/replace_directory_with_sub1
 		)
 	'
+	# Switching to a commit with nested submodules recursively checks them out
+	test_expect_success "$command: nested submodules are checked out" '
+		prolog &&
+		reset_work_tree_to_interested no_submodule &&
+		(
+			cd submodule_update &&
+			git branch -t modify_sub1_recursively origin/modify_sub1_recursively &&
+			$command modify_sub1_recursively &&
+			test_superproject_content origin/modify_sub1_recursively &&
+			test_submodule_content sub1 origin/modify_sub1_recursively &&
+			test_submodule_content -C sub1 sub2 origin/modify_sub1_recursively
+		)
+	'
 
 	######################## Disappearing submodule #######################
 	# Removing a submodule removes its work tree ...

unpack-trees.c

@@ -2060,7 +2060,7 @@ static int merged_entry(const struct cache_entry *ce,
 		}
 		invalidate_ce_path(merge, o);
 
-		if (submodule_from_ce(ce)) {
+		if (submodule_from_ce(ce) && file_exists(ce->name)) {
 			int ret = check_submodule_move_head(ce, NULL,
 							    oid_to_hex(&ce->oid),
 							    o);
@@ -2089,7 +2089,7 @@ static int merged_entry(const struct cache_entry *ce,
 			invalidate_ce_path(old, o);
 		}
 
-		if (submodule_from_ce(ce)) {
+		if (submodule_from_ce(ce) && file_exists(ce->name)) {
 			int ret = check_submodule_move_head(ce, oid_to_hex(&old->oid),
 							    oid_to_hex(&ce->oid),
 							    o);