Add a .gitignore and clean-up

[MakisH]

• Adds a central .gitignore, taking into account all solvers we currently support, and all rules we have already defined in cleaning-tools.sh.
• Adds individual .gitignore files in special cases, mainly where we download files from external repositories: aste-turbine, heat-exchanger.
• Restores some Make/ directory unintentionally deleted in Follow naming convention in partitioned heat conduction - FEniCS #459 and fixes the corresponding .gitignore. (cc @BenjaminRodenberg)

Also adds a comments on instructions to do a deep clean, as at the moment all externally downloaded files, python virtual environments, and C++ code builds are not deleted by the cleaning scripts (and one generally should not need to delete them). I already tried extending the cleaning scripts for this purpose, but it was easy to make them unnecessarily more complex.

Also, general cleanup:

• A stray reference-data is renamed to reference-results (cc @valentin-seitz)
• Improves the readability of the cleaning scripts, so that at least when everything is clean, one can easily see if something is wrong.
• Adds exceptions for the solver-* directories, to avoid the expected skipping messages.

@IshaanDesai @Fujikawas how do you like this change? Anything I have missed?

I did not really try running anything DUNE-related, but I guess it is covered.

closes #87

[Fujikawas]

but I guess it is covered.

Thank you doing this, I think all the folders and files to be removed relating to dunefem and dumux has been covered.

[IshaanDesai]

Looks good 👍

[fsimonis]

Looks all sane to me