Consolidate arguments and review unnecessary keyword arguments

[mcdigman]

Some functions have excessive amounts of arguments that makes them difficult to call and to create documentation. We need to review:

• which arguments really need to be keyword arguments and which don't, and if they are keyword arguments whether the defaults are reasonable
• which arguments should instead be passed as a config object
• which arguments are always or almost always used together and so can be consolidated into a more compact object

[mcdigman]

Nearly all of the core parameters are now stored in the config objects.