I've been doing a lot of refactorings involving moving classes between
modules. As a result of this I've noticed that the interface has some
big usability problems when it comes to this.
If I use cut and paste to move files between modules I would expect it
to just work. Instead the interface completely ignores the fact that
I'm pasting into a different module. Instead I have to make sure
preserve source folders is unselected then rechoose the right
module/directory combination in a rather crowded "choose destination
directory" dialog box.
The first few times I did I ended up moving things into the right
package but the wrong project.
Obviously it's too late to have this fixed for 4.5 but please look into
this for 5.0.