Reorganize files

Remove separation between core functionality and plugins and instead organized the files by common functionality. Optional components are handled within each logical unit.

Suggested layout:

# reusable event algorithms
Algorithms/
# different detector implementations
Detectors/
# small examples and tests
Examples/
# framework core components
Framework/
# anything that reads/writes data
Io/
# mature tools, e.g. fatras
Tools/