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I recently had some trouble with an update which came about because the upgraded modules had been unpacked into /modules instead of /sites/all/modules
Paths should be intuitive, and while it's usual to have information in the README that is unexpected, it should not contain information that is contrary to expectations. A user looking at "modules" may expect that it is the place to unpack contributed modules. This violates the principle of least astonishment.
Since this is reserved for core matter, and it appears that Drupal in fact ignores any contributed modules placed in /modules, I suggest that a more suitable name for this is /core.