Teach mv to move submodules

index 16ce99b..1d3ef63 100644
@@ -118,55 +118,60 @@ int cmd_mv(int argc, const char **argv, const char *prefix)
 				&& lstat(dst, &st) == 0)
 			bad = _("cannot move directory over file");
 		else if (src_is_dir) {
-			const char *src_w_slash = add_slash(src);
-			int len_w_slash = length + 1;
-			int first, last;
-
-			modes[i] = WORKING_DIRECTORY;
-
-			first = cache_name_pos(src_w_slash, len_w_slash);
-			if (first >= 0)
-				die (_("Huh? %.*s is in index?"),
-						len_w_slash, src_w_slash);
-
-			first = -1 - first;
-			for (last = first; last < active_nr; last++) {
-				const char *path = active_cache[last]->name;
-				if (strncmp(path, src_w_slash, len_w_slash))
-					break;
-			}
-			free((char *)src_w_slash);
-
-			if (last - first < 1)
-				bad = _("source directory is empty");
-			else {
-				int j, dst_len;
-
-				if (last - first > 0) {
-					source = xrealloc(source,
-							(argc + last - first)
-							* sizeof(char *));
-					destination = xrealloc(destination,
-							(argc + last - first)
-							* sizeof(char *));
-					modes = xrealloc(modes,
-							(argc + last - first)
-							* sizeof(enum update_mode));
+			int first = cache_name_pos(src, length);
+			if (first >= 0) {
+				if (!S_ISGITLINK(active_cache[first]->ce_mode))
+					die (_("Huh? Directory %s is in index and no submodule?"), src);
+			} else {
+				const char *src_w_slash = add_slash(src);
+				int last, len_w_slash = length + 1;
+
+				modes[i] = WORKING_DIRECTORY;
+
+				first = cache_name_pos(src_w_slash, len_w_slash);
+				if (first >= 0)
+					die (_("Huh? %.*s is in index?"),
+							len_w_slash, src_w_slash);
+
+				first = -1 - first;
+				for (last = first; last < active_nr; last++) {
+					const char *path = active_cache[last]->name;
+					if (strncmp(path, src_w_slash, len_w_slash))
+						break;
 				}
-
-				dst = add_slash(dst);
-				dst_len = strlen(dst);
-
-				for (j = 0; j < last - first; j++) {
-					const char *path =
-						active_cache[first + j]->name;
-					source[argc + j] = path;
-					destination[argc + j] =
-						prefix_path(dst, dst_len,
-							path + length + 1);
-					modes[argc + j] = INDEX;
+				free((char *)src_w_slash);
+
+				if (last - first < 1)
+					bad = _("source directory is empty");
+				else {
+					int j, dst_len;
+
+					if (last - first > 0) {
+						source = xrealloc(source,
+								(argc + last - first)
+								* sizeof(char *));
+						destination = xrealloc(destination,
+								(argc + last - first)
+								* sizeof(char *));
+						modes = xrealloc(modes,
+								(argc + last - first)
+								* sizeof(enum update_mode));
+					}
+
+					dst = add_slash(dst);
+					dst_len = strlen(dst);
+
+					for (j = 0; j < last - first; j++) {
+						const char *path =
+							active_cache[first + j]->name;
+						source[argc + j] = path;
+						destination[argc + j] =
+							prefix_path(dst, dst_len,
+								path + length + 1);
+						modes[argc + j] = INDEX;
+					}
+					argc += last - first;
 				}
-				argc += last - first;
 			}
 		} else if (cache_name_pos(src, length) < 0)
 			bad = _("not under version control");

index 1d3ef63..68b7060 100644
@@ -9,6 +9,7 @@
 #include "cache-tree.h"
 #include "string-list.h"
 #include "parse-options.h"
+#include "submodule.h"
 
 static const char * const builtin_mv_usage[] = {
 	N_("git mv [options] <source>... <destination>"),

@@ -66,7 +67,7 @@ int cmd_mv(int argc, const char **argv, const char *prefix)
 		OPT_BOOLEAN('k', NULL, &ignore_errors, N_("skip move/rename errors")),
 		OPT_END(),
 	};
-	const char **source, **destination, **dest_path;
+	const char **source, **destination, **dest_path, **submodule_gitfile;
 	enum update_mode { BOTH = 0, WORKING_DIRECTORY, INDEX } *modes;
 	struct stat st;
 	struct string_list src_for_dst = STRING_LIST_INIT_NODUP;

@@ -85,6 +86,7 @@ int cmd_mv(int argc, const char **argv, const char *prefix)
 	source = internal_copy_pathspec(prefix, argv, argc, 0);
 	modes = xcalloc(argc, sizeof(enum update_mode));
 	dest_path = internal_copy_pathspec(prefix, argv + argc, 1, 0);
+	submodule_gitfile = xcalloc(argc, sizeof(char *));
 
 	if (dest_path[0][0] == '\0')
 		/* special case: "." was normalized to "" */

@@ -120,8 +122,14 @@ int cmd_mv(int argc, const char **argv, const char *prefix)
 		else if (src_is_dir) {
 			int first = cache_name_pos(src, length);
 			if (first >= 0) {
+				struct strbuf submodule_dotgit = STRBUF_INIT;
 				if (!S_ISGITLINK(active_cache[first]->ce_mode))
 					die (_("Huh? Directory %s is in index and no submodule?"), src);
+				strbuf_addf(&submodule_dotgit, "%s/.git", src);
+				submodule_gitfile[i] = read_gitfile(submodule_dotgit.buf);
+				if (submodule_gitfile[i])
+					submodule_gitfile[i] = xstrdup(submodule_gitfile[i]);
+				strbuf_release(&submodule_dotgit);
 			} else {
 				const char *src_w_slash = add_slash(src);
 				int last, len_w_slash = length + 1;

@@ -216,9 +224,12 @@ int cmd_mv(int argc, const char **argv, const char *prefix)
 		int pos;
 		if (show_only || verbose)
 			printf(_("Renaming %s to %s\n"), src, dst);
-		if (!show_only && mode != INDEX &&
-				rename(src, dst) < 0 && !ignore_errors)
-			die_errno (_("renaming '%s' failed"), src);
+		if (!show_only && mode != INDEX) {
+			if (rename(src, dst) < 0 && !ignore_errors)
+				die_errno (_("renaming '%s' failed"), src);
+			if (submodule_gitfile[i])
+				connect_work_tree_and_git_dir(dst, submodule_gitfile[i]);
+		}
 
 		if (mode == WORKING_DIRECTORY)
 			continue;

index 3f0a3f9..d96d187 100644
@@ -1004,3 +1004,34 @@ int merge_submodule(unsigned char result[20], const char *path,
 	free(merges.objects);
 	return 0;
 }
+
+/* Update gitfile and core.worktree setting to connect work tree and git dir */
+void connect_work_tree_and_git_dir(const char *work_tree, const char *git_dir)
+{
+	struct strbuf file_name = STRBUF_INIT;
+	struct strbuf rel_path = STRBUF_INIT;
+	const char *real_work_tree = xstrdup(real_path(work_tree));
+	FILE *fp;
+
+	/* Update gitfile */
+	strbuf_addf(&file_name, "%s/.git", work_tree);
+	fp = fopen(file_name.buf, "w");
+	if (!fp)
+		die(_("Could not create git link %s"), file_name.buf);
+	fprintf(fp, "gitdir: %s\n", relative_path(git_dir, real_work_tree,
+						  &rel_path));
+	fclose(fp);
+
+	/* Update core.worktree setting */
+	strbuf_reset(&file_name);
+	strbuf_addf(&file_name, "%s/config", git_dir);
+	if (git_config_set_in_file(file_name.buf, "core.worktree",
+				   relative_path(real_work_tree, git_dir,
+						 &rel_path)))
+		die(_("Could not set core.worktree in %s"),
+		    file_name.buf);
+
+	strbuf_release(&file_name);
+	strbuf_release(&rel_path);
+	free((void *)real_work_tree);
+}

index c7ffc7c..29e9658 100644
@@ -36,5 +36,6 @@ int merge_submodule(unsigned char result[20], const char *path, const unsigned c
 int find_unpushed_submodules(unsigned char new_sha1[20], const char *remotes_name,
 		struct string_list *needs_pushing);
 int push_unpushed_submodules(unsigned char new_sha1[20], const char *remotes_name);
+void connect_work_tree_and_git_dir(const char *work_tree, const char *git_dir);
 
 #endif

index d96d187..584f7de 100644
@@ -10,6 +10,7 @@
 #include "string-list.h"
 #include "sha1-array.h"
 #include "argv-array.h"
+#include "blob.h"
 
 static struct string_list config_name_for_path;
 static struct string_list config_fetch_recurse_submodules_for_name;

@@ -30,6 +31,51 @@ static struct sha1_array ref_tips_after_fetch;
  */
 static int gitmodules_is_unmerged;
 
+/*
+ * This flag is set if the .gitmodules file had unstaged modifications on
+ * startup. This must be checked before allowing modifications to the
+ * .gitmodules file with the intention to stage them later, because when
+ * continuing we would stage the modifications the user didn't stage herself
+ * too. That might change in a future version when we learn to stage the
+ * changes we do ourselves without staging any previous modifications.
+ */
+static int gitmodules_is_modified;
+
+
+int is_staging_gitmodules_ok()
+{
+	return !gitmodules_is_modified;
+}
+
+void stage_updated_gitmodules(void)
+{
+	struct strbuf buf = STRBUF_INIT;
+	struct stat st;
+	int pos;
+	struct cache_entry *ce;
+	int namelen = strlen(".gitmodules");
+
+	pos = cache_name_pos(".gitmodules", namelen);
+	if (pos < 0) {
+		warning(_("could not find .gitmodules in index"));
+		return;
+	}
+	ce = active_cache[pos];
+	ce->ce_flags = namelen;
+	if (strbuf_read_file(&buf, ".gitmodules", 0) < 0)
+		die(_("reading updated .gitmodules failed"));
+	if (lstat(".gitmodules", &st) < 0)
+		die_errno(_("unable to stat updated .gitmodules"));
+	fill_stat_cache_info(ce, &st);
+	ce->ce_mode = ce_mode_from_stat(ce, st.st_mode);
+	if (remove_cache_entry_at(pos) < 0)
+		die(_("unable to remove .gitmodules from index"));
+	if (write_sha1_file(buf.buf, buf.len, blob_type, ce->sha1))
+		die(_("adding updated .gitmodules failed"));
+	if (add_cache_entry(ce, ADD_CACHE_OK_TO_ADD|ADD_CACHE_OK_TO_REPLACE))
+		die(_("staging updated .gitmodules failed"));
+}
+
 static int add_submodule_odb(const char *path)
 {
 	struct strbuf objects_directory = STRBUF_INIT;

@@ -116,6 +162,11 @@ void gitmodules_config(void)
 				    !memcmp(ce->name, ".gitmodules", 11))
 					gitmodules_is_unmerged = 1;
 			}
+		} else if (pos < active_nr) {
+			struct stat st;
+			if (lstat(".gitmodules", &st) == 0 &&
+			    ce_match_stat(active_cache[pos], &st, 0) & DATA_CHANGED)
+				gitmodules_is_modified = 1;
 		}
 
 		if (!gitmodules_is_unmerged)

index 29e9658..244d5f5 100644
@@ -11,6 +11,8 @@ enum {
 	RECURSE_SUBMODULES_ON = 2
 };
 
+int is_staging_gitmodules_ok();
+void stage_updated_gitmodules(void);
 void set_diffopt_flags_from_submodule_config(struct diff_options *diffopt,
 		const char *path);
 int submodule_config(const char *var, const char *value, void *cb);

index 68b7060..7dd6bb4 100644
@@ -58,7 +58,7 @@ static struct lock_file lock_file;
 
 int cmd_mv(int argc, const char **argv, const char *prefix)
 {
-	int i, newfd;
+	int i, newfd, gitmodules_modified = 0;
 	int verbose = 0, show_only = 0, force = 0, ignore_errors = 0;
 	struct option builtin_mv_options[] = {
 		OPT__VERBOSE(&verbose, N_("be verbose")),

@@ -72,6 +72,7 @@ int cmd_mv(int argc, const char **argv, const char *prefix)
 	struct stat st;
 	struct string_list src_for_dst = STRING_LIST_INIT_NODUP;
 
+	gitmodules_config();
 	git_config(git_default_config, NULL);
 
 	argc = parse_options(argc, argv, prefix, builtin_mv_options,

@@ -125,6 +126,8 @@ int cmd_mv(int argc, const char **argv, const char *prefix)
 				struct strbuf submodule_dotgit = STRBUF_INIT;
 				if (!S_ISGITLINK(active_cache[first]->ce_mode))
 					die (_("Huh? Directory %s is in index and no submodule?"), src);
+				if (!is_staging_gitmodules_ok())
+					die (_("Please, stage your changes to .gitmodules or stash them to proceed"));
 				strbuf_addf(&submodule_dotgit, "%s/.git", src);
 				submodule_gitfile[i] = read_gitfile(submodule_dotgit.buf);
 				if (submodule_gitfile[i])

@@ -229,6 +232,8 @@ int cmd_mv(int argc, const char **argv, const char *prefix)
 				die_errno (_("renaming '%s' failed"), src);
 			if (submodule_gitfile[i])
 				connect_work_tree_and_git_dir(dst, submodule_gitfile[i]);
+			if (!update_path_in_gitmodules(src, dst))
+				gitmodules_modified = 1;
 		}
 
 		if (mode == WORKING_DIRECTORY)

@@ -240,6 +245,9 @@ int cmd_mv(int argc, const char **argv, const char *prefix)
 			rename_cache_entry_at(pos, dst);
 	}
 
+	if (gitmodules_modified)
+		stage_updated_gitmodules();
+
 	if (active_cache_changed) {
 		if (write_cache(newfd, active_cache, active_nr) ||
 		    commit_locked_index(&lock_file))

index 584f7de..b210685 100644
@@ -47,6 +47,39 @@ int is_staging_gitmodules_ok()
 	return !gitmodules_is_modified;
 }
 
+/*
+ * Try to update the "path" entry in the "submodule.<name>" section of the
+ * .gitmodules file. Return 0 only if a .gitmodules file was found, a section
+ * with the correct path=<oldpath> setting was found and we could update it.
+ */
+int update_path_in_gitmodules(const char *oldpath, const char *newpath)
+{
+	struct strbuf entry = STRBUF_INIT;
+	struct string_list_item *path_option;
+
+	if (!file_exists(".gitmodules")) /* Do nothing without .gitmodules */
+		return -1;
+
+	if (gitmodules_is_unmerged)
+		die(_("Cannot change unmerged .gitmodules, resolve merge conflicts first"));
+
+	path_option = unsorted_string_list_lookup(&config_name_for_path, oldpath);
+	if (!path_option) {
+		warning(_("Could not find section in .gitmodules where path=%s"), oldpath);
+		return -1;
+	}
+	strbuf_addstr(&entry, "submodule.");
+	strbuf_addstr(&entry, path_option->util);
+	strbuf_addstr(&entry, ".path");
+	if (git_config_set_in_file(".gitmodules", entry.buf, newpath) < 0) {
+		/* Maybe the user already did that, don't error out here */
+		warning(_("Could not update .gitmodules entry %s"), entry.buf);
+		return -1;
+	}
+	strbuf_release(&entry);
+	return 0;
+}
+
 void stage_updated_gitmodules(void)
 {
 	struct strbuf buf = STRBUF_INIT;

index 244d5f5..570d4d0 100644
@@ -12,6 +12,7 @@ enum {
 };
 
 int is_staging_gitmodules_ok();
+int update_path_in_gitmodules(const char *oldpath, const char *newpath);
 void stage_updated_gitmodules(void);
 void set_diffopt_flags_from_submodule_config(struct diff_options *diffopt,
 		const char *path);

index 68b7060..7dd6bb4 100644
@@ -58,7 +58,7 @@ static struct lock_file lock_file;
 
 int cmd_mv(int argc, const char **argv, const char *prefix)
 {
-	int i, newfd;
+	int i, newfd, gitmodules_modified = 0;
 	int verbose = 0, show_only = 0, force = 0, ignore_errors = 0;
 	struct option builtin_mv_options[] = {
 		OPT__VERBOSE(&verbose, N_("be verbose")),

@@ -72,6 +72,7 @@ int cmd_mv(int argc, const char **argv, const char *prefix)
 	struct stat st;
 	struct string_list src_for_dst = STRING_LIST_INIT_NODUP;
 
+	gitmodules_config();
 	git_config(git_default_config, NULL);
 
 	argc = parse_options(argc, argv, prefix, builtin_mv_options,

@@ -125,6 +126,8 @@ int cmd_mv(int argc, const char **argv, const char *prefix)
 				struct strbuf submodule_dotgit = STRBUF_INIT;
 				if (!S_ISGITLINK(active_cache[first]->ce_mode))
 					die (_("Huh? Directory %s is in index and no submodule?"), src);
+				if (!is_staging_gitmodules_ok())
+					die (_("Please, stage your changes to .gitmodules or stash them to proceed"));
 				strbuf_addf(&submodule_dotgit, "%s/.git", src);
 				submodule_gitfile[i] = read_gitfile(submodule_dotgit.buf);
 				if (submodule_gitfile[i])

@@ -229,6 +232,8 @@ int cmd_mv(int argc, const char **argv, const char *prefix)
 				die_errno (_("renaming '%s' failed"), src);
 			if (submodule_gitfile[i])
 				connect_work_tree_and_git_dir(dst, submodule_gitfile[i]);
+			if (!update_path_in_gitmodules(src, dst))
+				gitmodules_modified = 1;
 		}
 
 		if (mode == WORKING_DIRECTORY)

@@ -240,6 +245,9 @@ int cmd_mv(int argc, const char **argv, const char *prefix)
 			rename_cache_entry_at(pos, dst);
 	}
 
+	if (gitmodules_modified)
+		stage_updated_gitmodules();
+
 	if (active_cache_changed) {
 		if (write_cache(newfd, active_cache, active_nr) ||
 		    commit_locked_index(&lock_file))

index 5874d08..1c2714f 100644
@@ -47,6 +47,40 @@ int is_staging_gitmodules_ok(void)
 	return !gitmodules_is_modified;
 }
 
+/*
+ * Try to update the "path" entry in the "submodule.<name>" section of the
+ * .gitmodules file. Return 0 only if a .gitmodules file was found, a section
+ * with the correct path=<oldpath> setting was found and we could update it.
+ */
+int update_path_in_gitmodules(const char *oldpath, const char *newpath)
+{
+	struct strbuf entry = STRBUF_INIT;
+	struct string_list_item *path_option;
+
+	if (!file_exists(".gitmodules")) /* Do nothing without .gitmodules */
+		return -1;
+
+	if (gitmodules_is_unmerged)
+		die(_("Cannot change unmerged .gitmodules, resolve merge conflicts first"));
+
+	path_option = unsorted_string_list_lookup(&config_name_for_path, oldpath);
+	if (!path_option) {
+		warning(_("Could not find section in .gitmodules where path=%s"), oldpath);
+		return -1;
+	}
+	strbuf_addstr(&entry, "submodule.");
+	strbuf_addstr(&entry, path_option->util);
+	strbuf_addstr(&entry, ".path");
+	if (git_config_set_in_file(".gitmodules", entry.buf, newpath) < 0) {
+		/* Maybe the user already did that, don't error out here */
+		warning(_("Could not update .gitmodules entry %s"), entry.buf);
+		strbuf_release(&entry);
+		return -1;
+	}
+	strbuf_release(&entry);
+	return 0;
+}
+
 void stage_updated_gitmodules(void)
 {
 	struct strbuf buf = STRBUF_INIT;

index 5501354..e339891 100644
@@ -12,6 +12,7 @@ enum {
 };
 
 int is_staging_gitmodules_ok(void);
+int update_path_in_gitmodules(const char *oldpath, const char *newpath);
 void stage_updated_gitmodules(void);
 void set_diffopt_flags_from_submodule_config(struct diff_options *diffopt,
 		const char *path);

index df85f98..a9d45dd 100644
@@ -283,6 +283,7 @@ int cmd_rm(int argc, const char **argv, const char *prefix)
 	struct pathspec pathspec;
 	char *seen;
 
+	gitmodules_config();
 	git_config(git_default_config, NULL);
 
 	argc = parse_options(argc, argv, prefix, builtin_rm_options,

@@ -324,7 +325,10 @@ int cmd_rm(int argc, const char **argv, const char *prefix)
 			continue;
 		ALLOC_GROW(list.entry, list.nr + 1, list.alloc);
 		list.entry[list.nr].name = ce->name;
-		list.entry[list.nr++].is_submodule = S_ISGITLINK(ce->ce_mode);
+		list.entry[list.nr].is_submodule = S_ISGITLINK(ce->ce_mode);
+		if (list.entry[list.nr++].is_submodule &&
+		    !is_staging_gitmodules_ok())
+			die (_("Please, stage your changes to .gitmodules or stash them to proceed"));
 	}
 
 	if (pathspec.nr) {

@@ -396,13 +400,15 @@ int cmd_rm(int argc, const char **argv, const char *prefix)
 	 * in the middle)
 	 */
 	if (!index_only) {
-		int removed = 0;
+		int removed = 0, gitmodules_modified = 0;
 		for (i = 0; i < list.nr; i++) {
 			const char *path = list.entry[i].name;
 			if (list.entry[i].is_submodule) {
 				if (is_empty_dir(path)) {
 					if (!rmdir(path)) {
 						removed = 1;
+						if (!remove_path_from_gitmodules(path))
+							gitmodules_modified = 1;
 						continue;
 					}
 				} else {

@@ -410,9 +416,14 @@ int cmd_rm(int argc, const char **argv, const char *prefix)
 					strbuf_addstr(&buf, path);
 					if (!remove_dir_recursively(&buf, 0)) {
 						removed = 1;
+						if (!remove_path_from_gitmodules(path))
+							gitmodules_modified = 1;
 						strbuf_release(&buf);
 						continue;
-					}
+					} else if (!file_exists(path))
+						/* Submodule was removed by user */
+						if (!remove_path_from_gitmodules(path))
+							gitmodules_modified = 1;
 					strbuf_release(&buf);
 					/* Fallthrough and let remove_path() fail. */
 				}

@@ -424,6 +435,8 @@ int cmd_rm(int argc, const char **argv, const char *prefix)
 			if (!removed)
 				die_errno("git rm: '%s'", path);
 		}
+		if (gitmodules_modified)
+			stage_updated_gitmodules();
 	}
 
 	if (active_cache_changed) {

index b210685..5cd8845 100644
@@ -80,6 +80,38 @@ int update_path_in_gitmodules(const char *oldpath, const char *newpath)
 	return 0;
 }
 
+/*
+ * Try to remove the "submodule.<name>" section from .gitmodules where the given
+ * path is configured. Return 0 only if a .gitmodules file was found, a section
+ * with the correct path=<path> setting was found and we could remove it.
+ */
+int remove_path_from_gitmodules(const char *path)
+{
+	struct strbuf sect = STRBUF_INIT;
+	struct string_list_item *path_option;
+
+	if (!file_exists(".gitmodules")) /* Do nothing without .gitmodules */
+		return -1;
+
+	if (gitmodules_is_unmerged)
+		die(_("Cannot change unmerged .gitmodules, resolve merge conflicts first"));
+
+	path_option = unsorted_string_list_lookup(&config_name_for_path, path);
+	if (!path_option) {
+		warning(_("Could not find section in .gitmodules where path=%s"), path);
+		return -1;
+	}
+	strbuf_addstr(&sect, "submodule.");
+	strbuf_addstr(&sect, path_option->util);
+	if (git_config_rename_section_in_file(".gitmodules", sect.buf, NULL) < 0) {
+		/* Maybe the user already did that, don't error out here */
+		warning(_("Could not remove .gitmodules entry for %s"), path);
+		return -1;
+	}
+	strbuf_release(&sect);
+	return 0;
+}
+
 void stage_updated_gitmodules(void)
 {
 	struct strbuf buf = STRBUF_INIT;

index 570d4d0..eca1d11 100644
@@ -13,6 +13,7 @@ enum {
 
 int is_staging_gitmodules_ok();
 int update_path_in_gitmodules(const char *oldpath, const char *newpath);
+int remove_path_from_gitmodules(const char *path);
 void stage_updated_gitmodules(void);
 void set_diffopt_flags_from_submodule_config(struct diff_options *diffopt,
 		const char *path);

index df85f98..a9d45dd 100644
@@ -283,6 +283,7 @@ int cmd_rm(int argc, const char **argv, const char *prefix)
 	struct pathspec pathspec;
 	char *seen;
 
+	gitmodules_config();
 	git_config(git_default_config, NULL);
 
 	argc = parse_options(argc, argv, prefix, builtin_rm_options,

@@ -324,7 +325,10 @@ int cmd_rm(int argc, const char **argv, const char *prefix)
 			continue;
 		ALLOC_GROW(list.entry, list.nr + 1, list.alloc);
 		list.entry[list.nr].name = ce->name;
-		list.entry[list.nr++].is_submodule = S_ISGITLINK(ce->ce_mode);
+		list.entry[list.nr].is_submodule = S_ISGITLINK(ce->ce_mode);
+		if (list.entry[list.nr++].is_submodule &&
+		    !is_staging_gitmodules_ok())
+			die (_("Please, stage your changes to .gitmodules or stash them to proceed"));
 	}
 
 	if (pathspec.nr) {

@@ -396,13 +400,15 @@ int cmd_rm(int argc, const char **argv, const char *prefix)
 	 * in the middle)
 	 */
 	if (!index_only) {
-		int removed = 0;
+		int removed = 0, gitmodules_modified = 0;
 		for (i = 0; i < list.nr; i++) {
 			const char *path = list.entry[i].name;
 			if (list.entry[i].is_submodule) {
 				if (is_empty_dir(path)) {
 					if (!rmdir(path)) {
 						removed = 1;
+						if (!remove_path_from_gitmodules(path))
+							gitmodules_modified = 1;
 						continue;
 					}
 				} else {

@@ -410,9 +416,14 @@ int cmd_rm(int argc, const char **argv, const char *prefix)
 					strbuf_addstr(&buf, path);
 					if (!remove_dir_recursively(&buf, 0)) {
 						removed = 1;
+						if (!remove_path_from_gitmodules(path))
+							gitmodules_modified = 1;
 						strbuf_release(&buf);
 						continue;
-					}
+					} else if (!file_exists(path))
+						/* Submodule was removed by user */
+						if (!remove_path_from_gitmodules(path))
+							gitmodules_modified = 1;
 					strbuf_release(&buf);
 					/* Fallthrough and let remove_path() fail. */
 				}

@@ -424,6 +435,8 @@ int cmd_rm(int argc, const char **argv, const char *prefix)
 			if (!removed)
 				die_errno("git rm: '%s'", path);
 		}
+		if (gitmodules_modified)
+			stage_updated_gitmodules();
 	}
 
 	if (active_cache_changed) {

index 1c2714f..35c745e 100644
@@ -81,6 +81,39 @@ int update_path_in_gitmodules(const char *oldpath, const char *newpath)
 	return 0;
 }
 
+/*
+ * Try to remove the "submodule.<name>" section from .gitmodules where the given
+ * path is configured. Return 0 only if a .gitmodules file was found, a section
+ * with the correct path=<path> setting was found and we could remove it.
+ */
+int remove_path_from_gitmodules(const char *path)
+{
+	struct strbuf sect = STRBUF_INIT;
+	struct string_list_item *path_option;
+
+	if (!file_exists(".gitmodules")) /* Do nothing without .gitmodules */
+		return -1;
+
+	if (gitmodules_is_unmerged)
+		die(_("Cannot change unmerged .gitmodules, resolve merge conflicts first"));
+
+	path_option = unsorted_string_list_lookup(&config_name_for_path, path);
+	if (!path_option) {
+		warning(_("Could not find section in .gitmodules where path=%s"), path);
+		return -1;
+	}
+	strbuf_addstr(&sect, "submodule.");
+	strbuf_addstr(&sect, path_option->util);
+	if (git_config_rename_section_in_file(".gitmodules", sect.buf, NULL) < 0) {
+		/* Maybe the user already did that, don't error out here */
+		warning(_("Could not remove .gitmodules entry for %s"), path);
+		strbuf_release(&sect);
+		return -1;
+	}
+	strbuf_release(&sect);
+	return 0;
+}
+
 void stage_updated_gitmodules(void)
 {
 	struct strbuf buf = STRBUF_INIT;

index e339891..7beec48 100644
@@ -13,6 +13,7 @@ enum {
 
 int is_staging_gitmodules_ok(void);
 int update_path_in_gitmodules(const char *oldpath, const char *newpath);
+int remove_path_from_gitmodules(const char *path);
 void stage_updated_gitmodules(void);
 void set_diffopt_flags_from_submodule_config(struct diff_options *diffopt,
 		const char *path);