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

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)

Before you request a review from someone, make sure to revise the following points:

• does the new code follow the style guide?
• do the test pipelines pass? (see guide on how to run pipelines for a merge request)
• does your change affect public interfaces or behavior, or, does it introduce a new feature? If so, document the change in CHANGELOG.md.
• all files have to end with a \n character. Make sure there is no \ No newline at end of file comment in "Changes" of this MR.