Update submodules with parent-tracked content

This updates how libgit2 treats submodule-like directories that
actually have tracked content inside of them.  This is a strange
corner case, but it seems that many people have abortive submodule
setups and then just went ahead and added the files into the
parent repository.  In this case, we should just treat the
submodule as if it was a normal directory.

Libgit2 will still try to skip over real submodules and contained
repositories that do not have tracked files inside them, but this
adds some new handling for cases where the apparently submodule
data is in conflict with the actual list of tracked files.

src/diff.c

@@ -876,7 +876,7 @@ static int handle_unmatched_new_item(
 			 DIFF_FLAG_IS_SET(diff, GIT_DIFF_RECURSE_IGNORED_DIRS));
 
 		/* do not advance into directories that contain a .git file */
-		if (recurse_into_dir) {
+		if (recurse_into_dir && !contains_oitem) {
 			git_buf *full = NULL;
 			if (git_iterator_current_workdir_path(&full, info->new_iter) < 0)
 				return -1;
@@ -969,6 +969,16 @@ static int handle_unmatched_new_item(
 		if (git_submodule_lookup(NULL, info->repo, nitem->path) != 0) {
 			giterr_clear();
 			delta_type = GIT_DELTA_IGNORED;
+
+			/* if this contains a tracked item, treat as normal TREE */
+			if (contains_oitem) {
+				error = git_iterator_advance_into(&info->nitem, info->new_iter);
+				if (error != GIT_ENOTFOUND)
+					return error;
+
+				giterr_clear();
+				return git_iterator_advance(&info->nitem, info->new_iter);
+			}
 		}
 	}
 

tests/status/submodules.c

 #include "clar_libgit2.h"
-#include "buffer.h"
-#include "path.h"
-#include "posix.h"
+#include "fileops.h"
 #include "status_helpers.h"
 #include "../submodule/submodule_helpers.h"
 
@@ -389,3 +387,92 @@ void test_status_submodules__contained_untracked_repo(void)
 		g_repo, &opts, cb_status__match, &counts));
 	cl_assert_equal_i(5, counts.entry_count);
 }
+
+void test_status_submodules__broken_stuff_that_git_allows(void)
+{
+	git_status_options opts = GIT_STATUS_OPTIONS_INIT;
+	status_entry_counts counts;
+	git_repository *contained;
+	static const char *expected_files_with_broken[] = {
+		".gitmodules",
+		"added",
+		"broken/tracked",
+		"deleted",
+		"ignored",
+		"modified",
+		"untracked"
+	};
+	static unsigned int expected_status_with_broken[] = {
+		GIT_STATUS_WT_MODIFIED,
+		GIT_STATUS_INDEX_NEW,
+		GIT_STATUS_INDEX_NEW,
+		GIT_STATUS_INDEX_DELETED,
+		GIT_STATUS_IGNORED,
+		GIT_STATUS_WT_MODIFIED,
+		GIT_STATUS_WT_NEW,
+	};
+
+	g_repo = setup_fixture_submodules();
+
+	opts.flags = GIT_STATUS_OPT_INCLUDE_UNTRACKED |
+		GIT_STATUS_OPT_RECURSE_UNTRACKED_DIRS |
+		GIT_STATUS_OPT_INCLUDE_IGNORED;
+
+	/* make a directory and stick a tracked item into the index */
+	{
+		git_index *idx;
+		cl_must_pass(p_mkdir("submodules/broken", 0777));
+		cl_git_mkfile("submodules/broken/tracked", "tracked content");
+		cl_git_pass(git_repository_index(&idx, g_repo));
+		cl_git_pass(git_index_add_bypath(idx, "broken/tracked"));
+		cl_git_pass(git_index_write(idx));
+		git_index_free(idx);
+	}
+
+	status_counts_init(
+		counts, expected_files_with_broken, expected_status_with_broken);
+	cl_git_pass(git_status_foreach_ext(
+		g_repo, &opts, cb_status__match, &counts));
+	cl_assert_equal_i(7, counts.entry_count);
+
+	/* directory with tracked items that looks a little bit like a repo */
+
+	cl_must_pass(p_mkdir("submodules/broken/.git", 0777));
+	cl_must_pass(p_mkdir("submodules/broken/.git/info", 0777));
+	cl_git_mkfile("submodules/broken/.git/info/exclude", "# bogus");
+
+	status_counts_init(
+		counts, expected_files_with_broken, expected_status_with_broken);
+	cl_git_pass(git_status_foreach_ext(
+		g_repo, &opts, cb_status__match, &counts));
+	cl_assert_equal_i(7, counts.entry_count);
+
+	/* directory with tracked items that is a repo */
+
+	cl_git_pass(git_futils_rmdir_r(
+		"submodules/broken/.git", NULL, GIT_RMDIR_REMOVE_FILES));
+	cl_git_pass(git_repository_init(&contained, "submodules/broken", false));
+	git_repository_free(contained);
+
+	status_counts_init(
+		counts, expected_files_with_broken, expected_status_with_broken);
+	cl_git_pass(git_status_foreach_ext(
+		g_repo, &opts, cb_status__match, &counts));
+	cl_assert_equal_i(7, counts.entry_count);
+
+	/* directory with tracked items that claims to be a submodule but is not */
+
+	cl_git_pass(git_futils_rmdir_r(
+		"submodules/broken/.git", NULL, GIT_RMDIR_REMOVE_FILES));
+	cl_git_append2file("submodules/.gitmodules",
+		"\n[submodule \"broken\"]\n"
+		"\tpath = broken\n"
+		"\turl = https://github.com/not/used\n\n");
+
+	status_counts_init(
+		counts, expected_files_with_broken, expected_status_with_broken);
+	cl_git_pass(git_status_foreach_ext(
+		g_repo, &opts, cb_status__match, &counts));
+	cl_assert_equal_i(7, counts.entry_count);
+}
+