By the way, if you changed the function prototype to this:

sub process ($\%\%) {
  my($path, $seen, $total) = @_;

  # do something...
}
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then you would (have to) call the function without putting a backslash before each hash:

my %seen;
my %total;

foreach my $path (@ARGV) {
  process($path, %seen, %total);
}
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The calling code specifies a bare hash, but Perl still puts a references to the hash in @_.

Personally, I prefer not to use prototypes; I would leave off the prototype definition and pass in explicit hash references.