For a while I used 'ToolAlias' to get around tools that weren't where project icons expected them to be. It worked well but was high maintenance to keep it's tool data up to date.
Like Xyth I now use Dopus to handle most of the filetyping but when the tool is moved, even Dopus needs to be retold where to find it.
I found DefTool, DeftoolManager, and Deft II (all in Aminet/util/wb) very useful. All are pretty easy to use but Deft II will work it's way through a directory tree making all the changes you ask, not just in the current directory.
Cheers
Andrew