Is there a tool for deploying things into exist? if I've got a bundle of, say, schemas and XQuery stored procedures? Is there a way of, say, bundling those into a zip or tar file and uploading them or deploying them into eXist?
Alternatively what is the best way of storing these things in a version controlled way (in a git repo, say) and deploying them to the eXist server? Ideally, it'd be nice to be able to have a simple script in a scripting language so you can simply call "deploy.py" or whatever and it'd take everything from the repository and load it into the XML database.
The EXpath packaging system specifies a format for generating a ZIP file with XQuery procedures (and other content) and deploying it into multiple XQuery databases.
See the specification. You should be able to use the Python zipfile module to generate these if you're inclined to use Python (though personally, I do so from a makefile).
Unfortunately, the process for checking currently installed package versions to upgrade if necessary is not standardized; I have a solution for BaseX, but nothing for eXist immediately at hand. However, eXist's implementation is well-documented, and you should have little trouble working with it.