Improve how Gradle handles Clojure and Python source files.

Use the idiomatic src/main/resources folder to put these on the
classpath, instead of manually putting them into a bin/ folder
that Eclipse is also trying to use. This avoids having Eclipse put
the class files it builds somewhere it also considers upstream.

Additional files that people have put in the src_clj or src_py
folders should be moved to src/main/resources.

Tested to make sure the Python console still works through Gradle,
Ant, and Eclipse.