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docs: groups and minor improvements

Tommaso Pecorella requested to merge tommypec/ns-3-dev:DoxyGroups into master

This is a spinoff of !1826, with only the fixes to the groups and some minor tweaks here and there.

Due to the rolling changes in the code, it's wiser to apply this one as soon as possible, so the code doesn't change too much under my feet. The other changes (mainly related to graphs and other fixes) are dependent on some bugs I'm trying to fix.

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