Such things are made possible by a function named make_clickable()1 that can be found in wp-includes/formatting.php. make_clickable() filters the comment_text hook with this:
The priority of 12 as used above simply tells WordPress to make links clickable for post contents after shortcodes are parsed (which is at priority 11). If you don’t like such behaviour, just change 12 to any number you want.
You should take a look at wp-includes/default-filters.php to choose an appropriate priority for make_clickable().
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