all "nexml.pm": Fixed subroutines calling "Bio::Phylo::IO->parse".
They were all using a '-file' argument, so Phylo created a new
filehandle every time even though an open filehandle for the file
was already available in $self. This meant that there were 2 open
filehandles for the same file, that the Phylo fh could not be
closed, and that temporary files could not be deleted after script
end. Changed it to use the '-handle' argument when possible.