Can I compile my document with other tools and use
latexmk -C only for cleaning up?
One application could be to use it then in the
clean: section of a
Makefile that uses
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Yes, you can use
latexmk -C (or
-c) just to clean up auxiliary files. By default,
-c cleans up the following files types:
@generated_exts = ( 'aux', 'bcf', 'fls', 'idx', 'ind', 'lof', 'lot', 'out', 'toc' );
latexmk.pl, l. 1088f)
-C also cleans up the actual output, i.e pdf, dvi, or what have you. If you want to add more file extensions to this list, have a look at https://tex.stackexchange.com/a/83386/4012.
latexmk -C /
-c can be run no matter how you initially compiled your document, and may very well be used only for cleanup.