Please have a look at https://github.com/magit/magit/pull/1268 and test it. I 
think that should do it for the time being.

With this *tracked* files are automatically reverted but only in the *current* 
repository and only after a *Magit command* did run. As such it mostly restores 
the behavior from a few months ago. It is less dangerous than that was because 
it ignores files that aren't tracked and those located in the gitdir. It still 
has the potential of eating data which is inherent to `revert-buffer'.

Never-the-less I am enabling it by default by default, because it restores the 
behavior we have had for years without anybody complaining.  Do you think I 
should not be doing that?

The behavior can be toggled using a global minor mode. By default that mode is 
active and has a mode-line lighter. The idea behind the "unnecessary" lighter 
is that this gives users a chance to notice it, click on it, and read about its 
implications.

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