Corrects check modules names in config on startup

[joaomcteixeira]

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Corrects the moment when the module's names are checked in the configuration file.

[codecov-commenter]

Codecov Report

Merging #477 (e460994) into main (5abbdf3) will not change coverage.
The diff coverage is 0.00%.

@@           Coverage Diff           @@
##             main     #477   +/-   ##
=======================================
  Coverage   72.22%   72.22%           
=======================================
  Files          95       95           
  Lines        6080     6080           
=======================================
  Hits         4391     4391           
  Misses       1689     1689           

Impacted Files	Coverage Δ
src/haddock/gear/prepare_run.py	45.86% <0.00%> (ø)

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