refactor create-directory-structure, and create 'clone_repo' function

See merge request mpsd-cs/mpsd-software-environments!35

Rename a few variables and function names for clarity

Closes #8

See merge request mpsd-cs/mpsd-software-environments!40

add CompletedProcess in logging of `run`

See merge request mpsd-cs/mpsd-software-environments!42

- in case of upcoming failure, this provides a clue in which function the
  failure is to find.

- it is only called once
- easier to have the code of the function in the place where it is called now

- also remove 'exact call:': that's kind of obvious

this is nice for debuging as it includes the information we want to obtain by
calling the command (such as branch name, commit hash, etc).

Restructure log location

Closes #7

See merge request mpsd-cs/mpsd-software-environments!29

Split logfile templates usage

See merge request mpsd-cs/mpsd-software-environments!39

Update log names and variable names

See merge request mpsd-cs/mpsd-software-environments!37

Rename log related variables

See merge request mpsd-cs/mpsd-software-environments!38