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The entire core/cache can be skipped in any backup or copying arrangement. MODX will regenerate them as needed when it runs.
Thank you. What about the cause of the problem? Any ideas why some files are copied normally and the others are not?
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No. I don't even have those files in any of my sites that I've look at, localhost, MODX Cloud or SkyToaster, so I have no idea what they are or where they come from.
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Ok, here's a reference that explains what they are, I always have minifyJS and minfyCSS turned off.
https://forums.modx.com/thread/88032/minify-cache-not-working
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Shocking the number of sites with web space file indexing turned on! A google search for core/cache/mgr/min was quite interesting.
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That was somebody's bright idea, that really isn't such a good idea after all. You can turn them off in the System Settings (compress_css and compress_js).
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The latest version of MODX also has a checkbox in the setup that allows you to have it on or off by default on installation.
I think Susan meant the compress_js and compress_css System Settings.
Go to System (gear icon in later versions) -> System Settings. Put compress in the search box at the upper right and press Enter.
Double click on the values and change them from 'Yes' to 'No'.