Refactor utility modules and test_utility.py

[alyssadai]

We have a growing number of *_utils.py modules for organizing utility functions shared across or specific to CLI commands. Currently, all these utility modules live in the same top-level directory as the main app (cli.py).

Meanwhile, we have a single test suite for all util functions, which is getting pretty big.

To better organize these util functions and their tests, we should:

• create a package called utility or utilities to store all *_utils.py files
• rename utility.py to utils.py for consistency w/ other modules
• split test_utility.py into util-specific test modules
• remove test_generate_context() since it replicates logic of function being tested and is hard to maintain
• refactor out merging of context + final dataset instance for output .jsonld file, which overlaps across commands (Originally posted by @surchs in [ENH] Add derivatives command and pipeline-catalog submodule #349 (comment))
• consider importing utils as a namespace instead of importing functions directly, for consistency w/ other modules
• One idea could be to export methods from across the utility modules from a utils package, i.e. in the __init__.py file. That way at least I could import them all as from utils import get_Something, getAnotherthing. Another idea could be to generally reduce the number of sub-modules for utility methods to something more manageable. (Originally posted by @surchs in [ENH] Update bagel bids to handle JSONLD inputs incl. derivative metadata #356 (review))