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[doc][doxygen] Update modules available for \ingroup, fix errors regarding \ingroup, fix errors regarding \file.

Melanie Lipp requested to merge cleanup/ingroups_and_modules into master

What this MR does / why does DuMux need it: This MR makes sure the modules in doc/doxygen/modules.txt match the current dumux folder structure. Wrong and missing ingroups are corrected. Missing \files are included, excess \files are removed.

Related to #1178 (closed)

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Edited by Melanie Lipp

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