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if ( m|/user/(?!prot/)| )

#!/usr/local/bin/perl5.6.0 -w
use strict;
...
/user/protrusions/
/user/a/
/user/backups

<LocationMatch  /user/(?!prot/) >
   <Limit GET>
...
    </Limit>
    AllowOverride None
</LocationMatch>