And with that comes the ability to rename sources from the project manager, or to move them around... and things like that.
The problem with this is that currently, that is quite hard to achieve. Projects work on files, and if a folder contains no project files you will not be able to see it.
Unless we do a major redesign, we'll have to resort to a hack to enable features like this. And even then, there won't be an easy way.
Think of cvs and .svn folders -- you would not want these to appear in the project view. The problem is that there are a couple more of them, and neither do we know about all of them, nor are they standardised (for example, TortoiseSVN came up with folders called _svn instead of .svn because of some Windows fallacy, and this is now official, but the only way to know which one is used on a particular machine is to query an environment variable, which is a hack again).
Thus, we would have to keep track of Code::Blocks generated directories ourselves inside the project file... or something. But that again, is no good solution.