Cleaned up IOManager public interface. MILESTONE.

MILESTONE: the public interface is now pretty much set.

    IOManager.edit()
    IOManager.execute_file()
    IOManager.invoke_shell()
    IOManager.interpret_file()
    IOManager.open_file()
    IOManager.run_command()
    IOManager.run_lilypond()
    IOManager.write()
    IOManager.write_stub()

We can expect essentially this same public interface for public deployment.