This isn’t a bug, it’s documented behaviour. From man git-clean:
If an untracked directory is managed by a different git repository, it is not removed by default.
The submod directory is a different git repository; if you want to remove it, Use -f option twice if you really want to remove such a directory.
git clean -f -f -d submod does remove submod. See my steps below (almost identical; different git version and hard-coded submodule path because otherwise git spits the dummy).
Steps
$ git --version
git version 1.7.5.4 # Note, different git-version.
Make the two repositories
git init submod
cd submod
echo "This is a submodule" > README.txt
git add .
git commit -m "Initial commit"
cd ..
git init prog
cd prog
echo "This is a program" > README.txt
git add .
git commit -a -m "Initial commit"
Add submod as a git submodule in topic1 branch.
git checkout -b topic1
git submodule add /Users/simont/sandbox/SOTESTING/Subdir-testing/submod
git commit -m "Added submodule"
Now for the interesting section.
$ git checkout master
warning: unable to rmdir submod: Directory not empty
Switched to branch 'master'
git status
# On branch master
# Untracked files:
# (use "git add ..." to include in what will be committed)
#
# submod/
#nothing added to commit but untracked files present (use "git add" to track)
Attempt to git-clean, then actually git-clean.
git clean -fd
#Removing submod/
git status
# On branch master
# Untracked files:
# (use "git add ..." to include in what will be committed)
#
# submod/
#nothing added to commit but untracked files present (use "git add" to track)
$ # As we can see, we haven't actually removed anything yet.
$ ls
README.txt submod
$ git clean -f -f -d submod
Removing submod/
$ ls
README.txt
$ git status
# On branch master
nothing to commit (working directory clean)