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You need also to specify the -jobname option when you use latexmk -c, i.e., latexmk -c -jobname=these header.tex

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Write a file called bw.cfg and containing \PassOptionsToPackage{monochrome}{xcolor} and modify your main file to have \InputIfFileExists{bw.cfg}{}{} before the call to xcolor. For printing in colors just rename the file. Full test document. \documentclass{article} \InputIfFileExists{bw.cfg}{}{} \usepackage{xcolor} \begin{document} Black ...

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(As the author of latexmk, I am naturally partial to my own program, but here's my 2-cents' worth anyway.) The fundamental problem that latexmk solves is that the number of runs of (pdf)latex needed is highly dynamically dependent on the document and the class file used. If you make a small change to a document, often only one recompilation by (pdf)latex ...

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