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[doc][doxygen] Cleanup, especially of modules.txt and ingroups.

Melanie Lipp requested to merge doc/doxygen_update_modules_txt_ingroups into master

Introduces new groups in modules.txt according to the changed folder structure. Corrects some ingroups. Removes some superfluous \file. Corrects other small doxygen issues (some missing documentation and some wrong copydoc reference).

Closes #1131 (closed)

Edited by Melanie Lipp

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