Fix template classes and rename

[s-martin]

Fix all the remaining template classes, i.e. move them from .C to header file.
This was already done for GAList, GATree, GAListGenome, GATreeGenome (see PR #5), but needs to be done for other classes, so all examples work.

Afterwards rename all the .h files with the template classes to .hpp.

[s-martin]

All examples work now, but some classes still need to be done.