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#1211 Clean-up Doxygen script

GILLES Sebastien requested to merge sgilles/MoReFEM:1211_doxygen into master
  • ModelInstances and Tests were left out of the generated documentation, which was a mistake.
  • LaTeX generation failed; even if LaTeX document is not very wieldy this highlights problems in my use of Doxygen (for instance putting code within a parameter doesn't give a good rendering either in html format).
  • Add a link to README.md for the main page
  • Provide three levels of documentation (basic, advanced, internal)
  • There was also the issue that output directory was related to my own account.

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