Problems when generating stubs due to interactions with user.clj

[cursive-ide]

When Cursive generates stubs, it currently creates a classpath for the module as if it were running a REPL. However, this can cause issues due to user.clj files which may be on the classpath and will be automatically executed by Clojure. Since stubs are only generated for library code, the classpath for stub generation should only include the library roots, and not source roots.