Apply update script to header, source and prm files.

[gassmoeller]

This PR applies the update script and also make the scripts a bit safer against accidental shell expansion. Together with #5941 this should also close #6006. If I apply the current update script against ASPECT main, no changes exept for the ones in this PR are made.

[gassmoeller]

Looks like a few tests were affected, because the update script no longer writes the name of the processed file when processing it. What I do not understand is how this bug passed the tester before. It was introduced in #6052 by forgetting to put a : after the number of particles output. I checked that there are many tests that include this output line. It looks like numdiff is ignoring the : sign? I only noticed because when I update the reference results of the failing tests in this PR manually it changed that line in the output. Anyway, it is fixed now, and only a cosmetic change anyway.

[gassmoeller]

@YiminJin you originally reported #6006, could you check if this branch fixes all the problems with the update scripts you observed?

[YiminJin]

@gassmoeller This PR has fixed the bug. I fetched it into my local repository and ran contrib/utilities/update_all_scripts.sh with a new script for ,prm file updating (the one I added for WENO limiter in #5929 ), and everything went well.

Thank you for addressing this issue!