Just came across this thread, felt like giving my "two cents":
As far as the IDE auto-lowercase feature is concerned, I've never cared enough either way for it to bother me or not bother me. However, I would tend to agree with "russdirks" in that there are certainly many situations where a project (especially one that consists of a high number of units and multiple developers) might benefit from a mixed-case naming scheme.
Secondly:
As much respect as I have for the Linux project as a whole, I certainly feel that the fact that it can't handle mixed-case filenames in 2016 is sheer insanity that should not be viewed by anyone as "ok" or "just how Linux is". It's just a missing feature. Nothing more. Little things like that are the reason people who are still honestly waiting for the "year of the Linux desktop" are likely to be waiting for a very, very long time.