> [...] any tips are welcome ;-)

I suggest to introduce the .gitignore file at the root level
with a directory that anyone can use for whatever. The reason
is that I would like to use some "private" subdirectory that
is near to doxygen's everything.

Sure, I can make my own fork, my own .gitignore, and I can
secretly decide what the name of the directory is to be.
However, the pull request/merge would not be that easy in such case.
The goal is to keep the .gitignore public. Because of that,
the private subdirectory should be named publicly.

It can be defined via prefix and the wildcard. I suggest 
to put the following line to the .gitignore:

__*/

i.e. two underscores, star, slash. This way, any directory
that starts with two underscores will be considered private.

This way, developers will be free to create whatever private
subdirectory they like, wherever they like.

The rule "the two-underscore prefix" is easy to explain.

Petr




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