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Apply update script to header, source and prm files. #6062

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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.

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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.

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contrib/utilities/update_scripts/source_files out of date
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