So I'm working on migrating back to Intellij to do some Groovy/Grails stuff (from Netbeans, but that's another long blog post if you're really interested).... I quickly realized the path-of-least-resistance was to just create a new Intellij project and copy over the stuff in the source folders. Since I was migrating from Grails 1.0.4 to 1.1Beta2 anyways I figured I'd clean up some cruft as well.
My main concern was how to re-sync with the existing Git remote repository I have hosting my project at Assembla's Git repo. I'm used to Subversion, which has those .svn directories in every sub-directory underneath your project root. I started mentally constructing a "find -name .git -exec mv ..." command in my brain. I found only one .git directory at the root of my project. I figured "what the hell, I'll just move the old .git dir into the new project dir and roll the dice."
git status
git commit .
git push
Done! Very nice indeed. For those running on Mac OSX here's a useful link for setting up a global .gitignore for those pesky .DS_Store files.
Also, here's a link for setting up a .gitignore for a Grails application.