When a submodule has its git dir inside the working dir, the submodule
support for checkout that we plan to add in a later patch will fail.

Add functionality to migrate the git directory to be embedded
into the superprojects git directory.

Signed-off-by: Stefan Beller <sbel...@google.com>
---
 Documentation/git-submodule.txt   | 14 +++++++
 builtin/submodule--helper.c       | 33 ++++++++++++++++-
 git-submodule.sh                  |  7 +++-
 submodule.c                       | 65 ++++++++++++++++++++++++++++++++
 submodule.h                       |  2 +
 t/t7412-submodule-embedgitdirs.sh | 78 +++++++++++++++++++++++++++++++++++++++
 6 files changed, 197 insertions(+), 2 deletions(-)
 create mode 100755 t/t7412-submodule-embedgitdirs.sh

diff --git a/Documentation/git-submodule.txt b/Documentation/git-submodule.txt
index d841573475..34791cfc65 100644
--- a/Documentation/git-submodule.txt
+++ b/Documentation/git-submodule.txt
@@ -22,6 +22,7 @@ SYNOPSIS
              [commit] [--] [<path>...]
 'git submodule' [--quiet] foreach [--recursive] <command>
 'git submodule' [--quiet] sync [--recursive] [--] [<path>...]
+'git submodule' [--quiet] embedgitdirs [--] [<path>...]
 
 
 DESCRIPTION
@@ -245,6 +246,19 @@ sync::
 If `--recursive` is specified, this command will recurse into the
 registered submodules, and sync any nested submodules within.
 
+embedgitdirs::
+       Move the git directory of submodules into its superprojects
+       `$GIT_DIR/modules` path and then connect the git directory and
+       its working directory by setting the `core.worktree` and adding
+       a .git file pointing to the git directory interned into the
+       superproject.
++
+A repository that was cloned independently and later added as a submodule or
+old setups have the submodules git directory inside the submodule instead of
+embedded into the superprojects git directory.
++
+This command is recursive by default.
+
 OPTIONS
 -------
 -q::
diff --git a/builtin/submodule--helper.c b/builtin/submodule--helper.c
index 806e29ce4e..e94dd68a0e 100644
--- a/builtin/submodule--helper.c
+++ b/builtin/submodule--helper.c
@@ -1076,6 +1076,36 @@ static int resolve_remote_submodule_branch(int argc, 
const char **argv,
        return 0;
 }
 
+static int embed_git_dir(int argc, const char **argv, const char *prefix)
+{
+       int i;
+       struct pathspec pathspec;
+       struct module_list list = MODULE_LIST_INIT;
+
+       struct option embed_gitdir_options[] = {
+               OPT_END()
+       };
+
+       const char *const git_submodule_helper_usage[] = {
+               N_("git submodule--helper embed-git-dir [<path>...]"),
+               NULL
+       };
+
+       argc = parse_options(argc, argv, prefix, embed_gitdir_options,
+                            git_submodule_helper_usage, 0);
+
+       gitmodules_config();
+       git_config(submodule_config, NULL);
+
+       if (module_list_compute(argc, argv, prefix, &pathspec, &list) < 0)
+               return 1;
+
+       for (i = 0; i < list.nr; i++)
+               migrate_submodule_gitdir(prefix, list.entries[i]->name, 1);
+
+       return 0;
+}
+
 #define SUPPORT_SUPER_PREFIX (1<<0)
 
 struct cmd_struct {
@@ -1093,7 +1123,8 @@ static struct cmd_struct commands[] = {
        {"resolve-relative-url", resolve_relative_url, 0},
        {"resolve-relative-url-test", resolve_relative_url_test, 0},
        {"init", module_init, 0},
-       {"remote-branch", resolve_remote_submodule_branch, 0}
+       {"remote-branch", resolve_remote_submodule_branch, 0},
+       {"embed-git-dirs", embed_git_dir, SUPPORT_SUPER_PREFIX}
 };
 
 int cmd_submodule__helper(int argc, const char **argv, const char *prefix)
diff --git a/git-submodule.sh b/git-submodule.sh
index a024a135d6..2178248287 100755
--- a/git-submodule.sh
+++ b/git-submodule.sh
@@ -1131,6 +1131,11 @@ cmd_sync()
        done
 }
 
+cmd_embedgitdirs()
+{
+       git submodule--helper --prefix "$wt_prefix" embed-git-dirs "$@"
+}
+
 # This loop parses the command line arguments to find the
 # subcommand name to dispatch.  Parsing of the subcommand specific
 # options are primarily done by the subcommand implementations.
@@ -1140,7 +1145,7 @@ cmd_sync()
 while test $# != 0 && test -z "$command"
 do
        case "$1" in
-       add | foreach | init | deinit | update | status | summary | sync)
+       add | foreach | init | deinit | update | status | summary | sync | 
embedgitdirs)
                command=$1
                ;;
        -q|--quiet)
diff --git a/submodule.c b/submodule.c
index 66c5ce5a24..d330b567a3 100644
--- a/submodule.c
+++ b/submodule.c
@@ -1263,3 +1263,68 @@ void prepare_submodule_repo_env(struct argv_array *out)
        }
        argv_array_push(out, "GIT_DIR=.git");
 }
+
+/*
+ * Migrate the given submodule (and all its submodules recursively) from
+ * having its git directory within the working tree to the git dir nested
+ * in its superprojects git dir under modules/.
+ */
+void migrate_submodule_gitdir(const char *prefix, const char *path,
+                             int recursive)
+{
+       char *old_git_dir;
+       const char *new_git_dir;
+       const struct submodule *sub;
+
+       old_git_dir = xstrfmt("%s/.git", path);
+       if (read_gitfile(old_git_dir))
+               /* If it is an actual gitfile, it doesn't need migration. */
+               goto out;
+
+       sub = submodule_from_path(null_sha1, path);
+       if (!sub)
+               die(_("Could not lookup name for submodule '%s'"),
+                     path);
+
+       new_git_dir = git_common_path("modules/%s", sub->name);
+       if (safe_create_leading_directories_const(new_git_dir) < 0)
+               die(_("could not create directory '%s'"), new_git_dir);
+
+       if (!prefix)
+               prefix = get_super_prefix();
+       printf("Migrating git directory of %s%s from\n'%s' to\n'%s'\n",
+               prefix ? prefix : "", path,
+               real_path(old_git_dir), new_git_dir);
+
+       if (rename(old_git_dir, new_git_dir) < 0)
+               die_errno(_("Could not migrate git directory from '%s' to 
'%s'"),
+                       old_git_dir, new_git_dir);
+
+       connect_work_tree_and_git_dir(path, new_git_dir);
+
+out:
+       if (recursive) {
+               struct child_process cp = CHILD_PROCESS_INIT;
+               struct strbuf sb = STRBUF_INIT;
+
+               if (get_super_prefix())
+                       strbuf_addstr(&sb, get_super_prefix());
+               strbuf_addstr(&sb, path);
+               strbuf_addch(&sb, '/');
+
+               cp.dir = path;
+               cp.git_cmd = 1;
+               cp.no_stdin = 1;
+               argv_array_pushl(&cp.args, "--super-prefix", sb.buf,
+                                           "submodule--helper",
+                                          "embed-git-dirs", NULL);
+               prepare_submodule_repo_env(&cp.env_array);
+               if (run_command(&cp))
+                       die(_("Could not migrate git directory in submodule 
'%s'"),
+                           path);
+
+               strbuf_release(&sb);
+       }
+
+       free(old_git_dir);
+}
diff --git a/submodule.h b/submodule.h
index d9e197a948..e5975d1f3d 100644
--- a/submodule.h
+++ b/submodule.h
@@ -75,4 +75,6 @@ int parallel_submodules(void);
  */
 void prepare_submodule_repo_env(struct argv_array *out);
 
+extern void migrate_submodule_gitdir(const char *prefix,
+                                    const char *path, int recursive);
 #endif
diff --git a/t/t7412-submodule-embedgitdirs.sh 
b/t/t7412-submodule-embedgitdirs.sh
new file mode 100755
index 0000000000..3153dbc069
--- /dev/null
+++ b/t/t7412-submodule-embedgitdirs.sh
@@ -0,0 +1,78 @@
+#!/bin/sh
+
+test_description='Test submodule embedgitdirs
+
+This test verifies that `git submodue embedgitdirs` moves a submodules git
+directory into the superproject.
+'
+
+. ./test-lib.sh
+
+test_expect_success 'setup a real submodule' '
+       git init sub1 &&
+       test_commit -C sub1 first &&
+       git submodule add ./sub1 &&
+       test_tick &&
+       git commit -m superproject
+'
+
+test_expect_success 'embed the git dir' '
+       >expect.1 &&
+       >expect.2 &&
+       >actual.1 &&
+       >actual.2 &&
+       git status >expect.1 &&
+       git -C sub1 rev-parse HEAD >expect.2 &&
+       git submodule embedgitdirs &&
+       git fsck &&
+       test -f sub1/.git &&
+       test -d .git/modules/sub1 &&
+       git status >actual.1 &&
+       git -C sub1 rev-parse HEAD >actual.2 &&
+       test_cmp expect.1 actual.1 &&
+       test_cmp expect.2 actual.2
+'
+
+test_expect_success 'setup nested submodule' '
+       git init sub1/nested &&
+       test_commit -C sub1/nested first_nested &&
+       git -C sub1 submodule add ./nested &&
+       test_tick &&
+       git -C sub1 commit -m "add nested" &&
+       git add sub1 &&
+       git commit -m "sub1 to include nested submodule"
+'
+
+test_expect_success 'embed the git dir in a nested submodule' '
+       git status >expect.1 &&
+       git -C sub1/nested rev-parse HEAD >expect.2 &&
+       git submodule embedgitdirs &&
+       test -f sub1/nested/.git &&
+       test -d .git/modules/sub1/modules/nested &&
+       git status >actual.1 &&
+       git -C sub1/nested rev-parse HEAD >actual.2 &&
+       test_cmp expect.1 actual.1 &&
+       test_cmp expect.2 actual.2
+'
+
+test_expect_success 'setup a gitlink with missing .gitmodules entry' '
+       git init sub2 &&
+       test_commit -C sub2 first &&
+       git add sub2 &&
+       git commit -m superproject
+'
+
+test_expect_success 'embedding the git dir fails for incomplete submodules' '
+       git status >expect.1 &&
+       git -C sub2 rev-parse HEAD >expect.2 &&
+       test_must_fail git submodule embedgitdirs &&
+       git -C sub2 fsck &&
+       test -d sub2/.git &&
+       git status >actual &&
+       git -C sub2 rev-parse HEAD >actual.2 &&
+       test_cmp expect.1 actual.1 &&
+       test_cmp expect.2 actual.2
+'
+
+test_done
+
-- 
2.11.0.rc2.4.g3396b6f.dirty

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