I've been burned by these kind of tools before, when I started using the CDPATH variable, as supported by bash.

Imagine the situation where you have a bunch of domains stored beneath /home/www. For example "/home/www/example.com" and "/home/www/example.org". (This is common for vhosts with a single prefix).

I decided I was going to get rid of the archived copies beneath /var/backup - so I decide to run "cd /var/backup; cd example.com; rm -rf *". Because of the path-searching I ended up at my live location, not my (obsolete) backup.

Since then I've always decided to navigate manually.