I have a somewhat complex project with multiple directories marked as "source folders" inside of each are collections of Python modules.
The problem I'm having is that PyCharm 3 and IDEA 13 + Python Plugin are not resolving all of the modules in these directories when they are referenced in :type: lines in docblocks.
The classes are resolved fine in the code itself and I can click-navigate – but they do not resolve in the docblocks. Simple types resolve, and classes within the same file resolve, but things like mod.submod.Class do not link to the declaration.
This problem disables code completion and other nice features, too.
The same exact project works perfectly in IDEA 12 + Python plugin.
Does anyone have any ideas what I'm doing wrong? Or where I can start looking to try to figure this out? It's really putting a damper on using the newer versions.