Fix search directories for clang-format

[stotko]

After adopting the pitchfork layout in #394, the search directories used to collect all files applicable for clang-format were not updated. Thus, the formatting script as well as the accompanying check script missed half of the project since then. Fix this issue and also include helper files.

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 97.46%. Comparing base (1523669) to head (0ba089c).
Report is 3 commits behind head on master.

Additional details and impacted files

@@            Coverage Diff             @@
##           master     #438      +/-   ##
==========================================
+ Coverage   97.34%   97.46%   +0.11%     
==========================================
  Files          32       32              
  Lines        2524     2602      +78     
==========================================
+ Hits         2457     2536      +79     
+ Misses         67       66       -1     

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