Fix some code issues, move devices to subdirectory, some clean up and documentation, etc.

Fix CIDs 10587, 10813, 10911, 10912, 10402, 10403, 10577, 10578, 10579, 10848, 10861, 10865, 10868, 10910.

Move classes inheriting from device to a subdirectory.
Make sure only protobuf library installed by fairsoft is used.
Cleanup FairMQDevice and fix some initialization list warnings.
Loop to duplicate input files in Sampler.
Add some documentation to FairMQ.