Users with custom [diff] configuration most certainly didn't intend it to make
mq lose changes. It could:

 * git is handled perfectly fine.

 * nobinary could make mq leave some files out from the patches.

 * noprefix could make mq itself (and probably also other tools) fail to apply
   patches without the usual a/b prefix.

 * ignorews, ignorewsamount, or ignoreblanklines could create patches with
   missing whitespace that could fail to apply correctly.

Thus, when refreshing patches, use patch.difffeatureopts, optionally with git
as before, but without the config options for whitespace and format changing
that most likely will cause loss or problems.

(patch.diffopts is just patch.difffeatureopts with all options enabled and can
be replaced with that.)