IMPORTANT: file naming & namespaces

Instead of naming files MpdTpcSomeClass / MpdEmcSomeClass we should place SomeClass into their appropriate namespaces

This would be major change, as it will make it impossible to place all header files into 1 include directory (this is how it works now). Whole build system will require redesign as well - in the long term there is no other option though. The sooner we do it, the less work we will have in the future.