Resolve "Restructure directories structure"

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Closes #77 (closed) and #73 (closed) We need proper multilayered directory structure.

INITIAL ANALYSIS

Directories which must be in the top level
- detectors (with each detector having its subdirectory. DONE: 2022-01-27)
- cmake
- config/gconfig
- generators
- geometry
- input
- macro/macros
- physics
- scriptsr

Undecided
- doxygen (right now, it is not working and we don't have resources to support/maintain this)
- clustering
- eventdisplay
- kalman
- lhetrack
- mcstack
- mpdbase
- mpddst
- mpdfield
- mpdpid
- passive
- shield_pack