Needed Code Refactoring

[andersy005]

It appears that for the last few months, we've accumulated some technical debt:

• Lack of necessary user-facing supporting documentation on how to extend intake-esm
• Delayed refactoring: more code was added without refactoring
• A few components have become tightly-coupled which resulted in situations where some functions are not modular, making the package not flexible enough to extend without code duplication

As more people are finding intake-esm useful for their own use cases, it would be nice to do some code refactoring soon in order to make intake-esm flexible enough to extend and use.

[matt-long]

Clean up test directory to clearly distinguish input from out, file types, etc.

[andersy005]

Addressed in #77