I've just spent some time (far longer than I anticipated!) on refactoring the way the Introjucer handles modules..
Previously, it had a concept of a "modules folder", where all the modules had to be stored, and you could set this folder for each exporter target. That was quite restrictive, and meant that you couldn't combine modules from different directories, so I've rewritten it to give each module its own path, and that path can be set differently in each exp
I've also rewritten the GUI so that the modules now appear in the config tree-view, and you can delete and add them from there - selecting the top-level of the modules tree shows a panel which lets you download and update modules from the website in a much more flexible way than before. You can also drag-and-drop module folders into the treeview to add them.
None of these changes should break any existing projects, but I've rewritten a huge amount of code, so please let me know if anything seems wrong! But please note that any .jucer files that get saved by this new version won't be backwards-compatible with previous introjucer versions.
The new structure gets it much closer to the goal of being able to offer automatic download/installation of 3rd-party modules, rather than just the juce ones.