streamline function scripts and input files in joint_dir

[bertozzivill]

• [x] standardize ' and "
• [x] standardize function names ("." vs "_")
• [x] move access_dev functions and 05_predict functions to general functions
• [x] save current joint_dir framework, rename as archive, update run_on_glcloud filepaths to be consistent
• [x] rename joint_dir files for clarity
• [x] rename column names for clarity
• [x] remove writing of "odd" rasters
• [x] readmes in old input dir
• [x] readmes in new input dir