Specify full path in #include.

This is required for an upcoming application.
It was already discussed in #89 and will come up
with more changes as the application grows. So
step by step all #includes will have the full
paths prepended.
[IO] Clarify which mesh file was read.
[ML] Specify full path for some includes.
Consistent copyright year 2012-2014.
Merge pull request #452 from endJunction/Cleanup

Cleanup