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after removing the default exfat-fuse package version 1.2.5 from my Debian Stretch system and replacing it with version 1.3.0, compiled from source, running mount using type exfat results to an unknown filesystem error. Checking with /proc/filesystems reveals that exfat is not listed.

Manually mounting exfat drives with mount.exfat works fine, the executables reside in /usr/local/sbin.

How can I configure mount to use mount.exfat when appropriate?

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Install or symlink it as /sbin/mount.exfat.

(I checked strace -f mount -t nosuchfs nowhere nowhere. It tries /sbin/mount.nosuchfs, /sbin/fs.d/mount.nosuchfs, and /sbin/fs/mount.nosuchfs only).

What's the worst that could happen :). If you forget and try to apt install exfat-fuse again, it's either going to give you a nice error message to remind you, or overwrite it.

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