[rubygems/rubygems] Fix `gem pristine` sometimes not resetting extensions

If `gem pristine foo` is run, and there's a default copy of foo, only
executables for it are reset. However, that was causing other copies of
`foo` to only reset executables, which is unexpected.

We should not modify `options[:only_executables]`, but respect its value
for every gem, and make sure special handling for default gems does not
leak to other gems.

https://github.com/rubygems/rubygems/commit/2c3039f1b0

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