I find it really annoying when applications I use keep creating their own folders in my Documents directory. Luckily some applications can be configured not to do it. Today I was fighting against Flash Builder, trying to make persuade it not to create workspace in Documents (I have separate folder for development).
Using File > Switch Workspace works for as long as you don’t delete the one created in Documents by default. It turns out, that you have to edit this file to make it work properly:
and change these properties to point to directory of your choice: