Assign directory to each ATQA::Plot - avoid "duplication name" warning

[lubynets]

Major change:
Before all the plots (TH1, TH2, TProfile) were created, filled then one created a proper TDirectory, moved to it and Write() a Plot. In this case if two objects have the same name (string), the Root produced Warning in <TROOT::Append>: Replacing existing TH1: myHistogramName (Potential memory leak).
Now it is solved due to SetDirectory() to each plot right after its definition. And then instead of Write() each plot just the output TFile is Write().
Minor changes:

1. Executable codes are propagated into install directory for documenting of the run.
2. Cosmetics of the code done: moved extensive writing of function implementations from Task.hpp to Task.cpp; addressed clang-tidy suggestions.