The issue is as follows: R0b0t1@host:~/devel/project$ git submodule add https://github.com/user/project -f Cloning into '/home/R0b0t1/devel/project/-f'... My .gitignore's first line is *, and then I explicitly allow things. Despite the presence of "project/" in the .gitignore the submodule command says it is ignored. The "force" flag is interpreted as a flag and also as the destination directory. It is possible the argument parsing code for other commands exhibits this error. R0b0t1.