Yes, you have to exclude a whole lot. You also need to exclude binary files (like database dumps and tarballs) that you have lying around in your project direct

Yes, you have to exclude a whole lot. You also need to exclude binary files (like database dumps and tarballs) that you have lying around in your project directory, because once TM accesses those files it will read everything into memory, and it seems particularly bad at doing that. Another problem with TM's built-in "find in project" is that it's not incremental. AckMate will list matches as it finds them, whereas TM will only return results once it's read everything.