I am on MacOSX El Capitan
why if I use the "~/" as part of the path to the modules this does not work?
It would be - in my opinion - more portable if I could use "~" in the path, as it would allow me for instance to specify a single path regardless of the username (or OS). Multiple collaborators on a single project could then just have the juce folder in ~/juce and not have to edit the .jucer file every time they checkout a newer version from e.g. a shared repo.
Additionally/alternatively, would it not be nice to be able to save a user-wide setting with a "Default" path for the juce/modules folder,so that it can be accessed by all the projects on a given machine?