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Can I remove a file in /etc/grub.d that was not created by me without it being overwritten? I'm using fedora if that matters.

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Can I remove a file in /etc/grub.d?

You can remove the files under /etc/grub.d (it doesn't harm the current configuration), but it is better to keep them it will be used by grub to correctly set the grub.cfg after executing grub-mkconfig or updating grub, there is no benefit to remove them.

here is the content of /etc/grub.d/Readme (From Debian):

All executable files in this directory are processed in shell expansion order.

  00_*: Reserved for 00_header.
  10_*: Native boot entries.
  20_*: Third party apps (e.g. memtest86+).

The number namespace in-between is configurable by system installer and/or
administrator.  For example, you can add an entry to boot another OS as
01_otheros, 11_otheros, etc, depending on the position you want it to occupy in
the menu; and then adjust the default setting via /etc/default/grub.

ls /etc/grub.d:

00_header        10_linux      30_os-prober      40_custom  README
05_debian_theme  20_linux_xen  30_uefi-firmware  41_custom

The must known /etc/grub.d/40_custom file is used to manually adding a custom grub entry to grub.cfg.

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