Adjust docs for default repo config cli options

[mzuehlke]

Adjust docs for changes to the cli options when introducing default repo config

see #2337
closes #2344

[codecov]

Codecov Report

Merging #2360 (fdc8b6f) into master (1b0a4a4) will not change coverage.
The diff coverage is n/a.

@@           Coverage Diff           @@
##           master    #2360   +/-   ##
=======================================
  Coverage   80.26%   80.26%           
=======================================
  Files         138      138           
  Lines        2387     2387           
  Branches       54       54           
=======================================
  Hits         1916     1916           
  Misses        471      471           

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[fthomas]

Thanks Marco! I think we can also close #2344 when merging this.