I'd rather have each module have its own dependencies as subdirectories, sort of like node_modules. Everyone resolves paths from cwd.
If someone wants to share the same jquery across subdirs, I'm sure http redirects could be configured. Or alternately some sort of corporate versioning convention that developers can expect to have with absolute paths. Certainly better than ../jquery.
../package-name/ works with multiple apps on the same server, and mounted in other places than root. It's working quite well for us with HTML imports.