pdflatex doxygen flags added

[Stefan Csomor]

Hi

I=B9ve done a test generating the pdf files, I tried using a separate inclu=
de
file to have maximal configurability some links in the first chapter are not
generated correctly, but this doesn=B9t seem to be a problem that depends on
the include.

I haven=B9t added it to =8Call=B9 so you need regen.sh latex

Best,

Stefan
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