Directory structure in a computational physics project

Question

Current situation

My scientific project contains mainly various analytical and numerical calculations with a physical purpose, i.e. I work with Mathematica, MATLAB, Fortran. Of course, it would be nice to record progress using a version control program such as git.

I asked some friends what would be the best way to structure my files. In addition to the simple and well-known programmer file structure ( /bin/, /dat/, /doc/, /src/, ...), I have not found satisfactory, but similar answers:

• What is the best project structure for a Python application?
• Directory structure for C ++ library
• typical web application folder structure (Django)
• The correct folder structure for a large number of source files
• https://stackoverflow.com/q/7715704/2062965

I hope this problem does not close, because the physicist asks it;), as I believe, many scientists are faced with the same question at some point in more or less expansion. Knowing that programmers have encountered such problems before, I do not ask this question in Physical Stack Exchange , where it can be marked as off-topicor too broad.

Example

In my last project, I had the following global structure in which I had some interaction between the various elements of the project:

/External_Code_Contribution/
/Experimental_Data/
/Analytical_Calculations/
  /Project_Issue_1/
  /Project_Issue_5/
/Documentations/
  /Thesis/
  /Papers/
  /Talks/
/Literature/
/Project_Organization/
/Numerical_Calculations/
  /Project_Issue_1/
    /SubIssue_A/
    /SubIssue_B/
    /SubIssue_C/
  /Project_Issue_2/
  /Project_Issue_3/
  /Project_Issue_4/
  /Project_Issue_6/

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