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Reference update + minor fixes

Koen Wolters requested to merge kwolters/allpix-squared:master into master

Searching for allpix squared on Google I noticed that the reference somehow shows up at the top (above any other part of the website...). However the reference did not contain any link to the website or other parts of the documentation to follow. This MR changes that.

I also updated some parts where the Doxygen was incorrect and while doing this I also added some other minor fixes (mostly some structure in the dfise converter).

Edited by Koen Wolters

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