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Restructure directories structure

This issue is a proposal how to solve the milestone %Redesign current directories to reflect multi-layered structure.

Proposed restructuring of directories. Idea is to put directories (libraries) of same function into same subfolder (core, simulation, tracking) directories.pdf

Current state of cross-library dependencies. Arrow points to directory (library) that uses (links) source, e.g. mpdBase->kalman shows that kalman links (uses) source from directory mpdBase modules.pdf. Color distinguishes different directory (library) types: blue - core libraries, green - tracking, red - detectors, violet - Monte Carlo, coral - to remove/integrate.

As a part of this effort, file/library naming convention should be agreed on (e.g., mpdbase can be changed to mpdBase as it would be easier to read). I did not find any file/library naming convention. It is somewhere?

@roleg @hnatics

Edited by Jan Busa
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