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Update EXCLUDE_PATTERNS in the doxyfile #1033

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See commit messages for justification.

Checklist
  • contribution does not duplicate one of our existing pull requests
  • contribution is in a branch rebased against master
  • code compiles successfully without errors
  • documentation added/updated/removed where necessary
  • commits are logically organised and have good commit messages

While doxygen appears to not recognize some of the commands in the code's
comments, I feel it is more useful to have the classes available in the
generated documentation even if it is not entirely formatted correctly.
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