Allow designers to switch templates by modifying the template_file variable which as it is passed through _phptemplate_variables();

Additional handling of sidebars. Variables block_seqid and block_zebra are reset
for left and right columns. Seqid and Zebra still exist for all blocks in sequence.

Pass zebra and seqid variables to all templates by default (as explained here : http://drupal.org/node/16383)
Make the node object available to the page template on node views.

Removed the old style link parsing
Some small updates to work with 4.6
Checks for node-$type.tpl.php, so you can seperately theme story and blog nodes, for instance. Practically I think css is still better.
Loads favicon.ico when found in the theme directory. (this was there already, although it was broken)

fixing the problem whereby you couldn't link to an external link, and the inability to have a title tag.

Also does some regular expressions to prepopulate the form with the links from
link_page.

Fixes the problem whereby an empty array is always passed to secondary_links and primary_links, causing
the templates to print out a empty link.

  easier.

fixes a problem with the $terms variable, removes some more cruft from 4.4 , and makes user pictures work as expected.

- fixes duplicate comment anchor/ID
- fixes 'new' comment marker display - now appear
- fixes comment titles - now appear