If you are developing on a linux or a mac box, a workaround would be, to create subfolders which include symbolic links to your layoutfiles. Just use the ln command with -s
ln -s PATH_TO_YOUR_FILE
The Problem with this is, that your Layout folder still contains all the .xml files. But you could although select them by using the sub-folders. It's the closest thing, to what you would like to have.
I just read, that this might work with Windows, too if you are using Vista or later. There is this mklink command. Just google it, have never used it myself.
Another problem is, if you have the file opened and try to open it again out the plugin throws a NULL Pointer Exception. But it does not hang up.
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