PCGen license issues
Part of the problem with PCGen, and the core of what has enabled third parties to create patches for PCGen which both violate PCGen’s license and break PCGen itself, is the setting for “PCGen System Files” under “Preferences”.
It was a mistake for PCGen to allow third-parties to override portions of PCGen’s system files — particularly when PCGen itself is a LGPL product, and the third-party system files may not be. A third party who overwrites PCGen’s system files with non-(L)GPL code would be flagrantly violating the license (sections 5 and 6, specifically). It is obviously not in PCGen’s best interests to encourage violation of the license under which PCGen is released. If someone wants to create a derivative work of PCGen, they should fork the project and release their own application, not back-door the LGPL by patching PCGen.
License issues aside, allowing third-parties to override PCGen’s system files will inevitably result in incompatible versions of PCGen running around, some of which have standard system files and some of which don’t, causing user confusion and data set incompatibility. A bad scene, any way you look at it. Bad for PCGen, bad for PCGen’s users, bad for everyone.
(Incidentally, PCGen should be released under the GPL, not the LGPL: the LGPL is not appropriate for a stand-alone application like PCGen. But that’s kind of beside the point.)
Ultimately, it is the responsibility of the PCGen copyright owner(s) to make sure that third parties comply with the license under which PCGen is released. If they choose not to do so (and it appears that they are perfectly happy releasing PCGen under an inappropriate license, and having third parties flagrantly violate PCGen’s license), then there is nothing that anyone else can do about it.
C’est la vie.
The best that users of PCGen can do is be forewarned: do not install any third-party product which requires overriding the PCGen system files. It will cause nothing but problems.