Recently while setting up my vimfiles for version control I encountered a problem with git submodules. The plugins are included as git submodules and loaded up with pathogen. For those interested in details on how this works, there is a Vimcast available on this topic. Some of the plugins need to generate helptags or other files that will mark the working tree dirty. There is a very simple way to prevent this, but it is a little tricky to find out what is needed to make it work, that’s why I decided to write a blog post about how to do this.