git diff --name-only --diff-filter=D -z | xargs -0 git rm --cached
----------------
-Submodules
-~~~~~~~~~~
+SUBMODULES
+----------
Only submodules using a gitfile (which means they were cloned
with a Git version 1.7.8 or newer) will be removed from the work
tree, as their repository lives inside the .git directory of the
superproject. If a submodule (or one of those nested inside it)
still uses a .git directory, `git rm` will fail - no matter if forced
-or not - to protect the submodule's history.
+or not - to protect the submodule's history. If it exists the
+submodule.<name> section in the linkgit:gitmodules[5] file will also
+be removed and that file will be staged (unless --cached or -n are used).
A submodule is considered up-to-date when the HEAD is the same as
recorded in the index, no tracked files are modified and no untracked
(i.e. you are listing the files explicitly), it
does not remove `subdir/git-foo.sh`.
+BUGS
+----
+Each time a superproject update removes a populated submodule
+(e.g. when switching between commits before and after the removal) a
+stale submodule checkout will remain in the old location. Removing the
+old directory is only safe when it uses a gitfile, as otherwise the
+history of the submodule will be deleted too. This step will be
+obsolete when recursive submodule update has been implemented.
+
SEE ALSO
--------
linkgit:git-add[1]