Remove qiime_scripts_dir and python_exe_fp

Removed ```qiime_scripts_dir``` and ```python_exe_fp``` from the QIIME config file. This simplifies the QIIME installation process and makes a pip-installed QIIME closer to being functional out-of-the-box.

Fixes #1338.

Do we want ```cloud_environment``` and ```working_dir``` to be removed in this pull request as well? The docs state that ```working_dir``` might be deprecated in favor of ```temp_dir``` in QIIME 1.8.0. May be a good time to take care of these now.