If you don't want TT to add whitespace to your output, you can also use the PRE_CHOMP or POST_CHOMP directives when you make your Template object.

My Template (2.802.14) doesn't seem to mind multiple [% END %] directives on the same line. Perhaps something else was going on in your code?

#!/usr/bin/perl

use Template;

my $tt = Template->new;

my $template = <<"HERE";
<a[% IF url %] href="[% url %]"[% END %][% IF active %] class="active"
+[% END %]>
HERE

$tt->process( 
    \$template, 
    { url => 'http://www.example.com', active => 1 } 
    );

$tt->process( 
    \$template, 
    { url => 'http://www.example.com', active => 0 } 
    );
[download]

As for ttree, you can specify the config file with the -f switch. Are you playing with an older TT, by any chance?