Is it not possible to use subfolders in the Objects/ folder? I thought I would be clever and organize all my xml files by object type, but once I did that it no longer seems to recognize the dependencies (e.g. if an advanced pdf template depends upon a saved search, I get an error saying the saved search object cannot be found even though it's just in a different subfolder)

You can use subfolders, yes. What does your

deploy.xml

look like?

Ok I figured out why it wasn't working for me. I've been trying to figure out how to exclude certain objects from

project:deploy

and I thought I could accomplish this by only including certain object types in the deployment. But the problem is, if one of the objects included in my deployment depends on an object in the folders I'm not deploying, SDF doesn't see them. I think the solution may be to simply add those dependencies in the

manifest.xml

^ This is the way