Improve variable names

[ZoeRichter]

There is a list of variable and function names that should be changed for clarity, but are in enough places that it's very likely you might miss one and break something, so this should be done in a branch on its own.

Also, this means that the PR for updating names should only have variable name changes, which makes them easier to workshop/suggest/change in the PR

• all *_fname variables -> *_file
• all *_temp variables -> *_template
• outtake -> outlet
• intake -> inlet
• add _ prefix to functions and methods that should be private
• change 'up' and 'low' to 'min' and 'max' in the boundary box dimension dicts (item can also be checked off it the data structure for x_b, y_b, z_b changes, making this change inapplicable

[ZoeRichter]

Note from coffee chat: check into using the sed command to find and replace across multiple files at once w/ regex