[SYNPY-1437] INCOMPLETE/DRAFT - Start the process to move to use the /bundle2 rest API

[BryanFauble]

NOTE: This is an incomplete solution. All the changes included here are largely un-tested. Development on this jira stopped when I re-discovered that https://sagebionetworks.jira.com/browse/PLFM-8313 blocks us from being able to move to the /bundle2 rest APIs, as this prevents our ability to forcefully increment entities as available in an API like https://rest-docs.synapse.org/rest/PUT/entity/id.html

Problem:

• All resources that get saved to the Synapse rest API go through a multiple step process to store the entity data, annotations, activity, and association to the entity via several disjointed HTTP calls. APIs like https://rest-docs.synapse.org/rest/PUT/entity/id/bundle2.html and https://rest-docs.synapse.org/rest/POST/entity/bundle2/create.html exist to update or create everything (But activity, as it is a separate call) in a single HTTP request.
• By swapping to use the /bundle2 rest API we can consolidate the storing process for all OOP models and remove duplicated code across the code base.

Solution:

• Starts the process to implement all of the required logic to point the storing of all entities at the /bundle2 API calls
• Start to drop all usage of the core (And soon to be deprecated/removed) Synapse class functionality in favor or dedicated API call functions

Testing:

• TODO

[BryanFauble]

To be addressed

[BryanFauble]

update functionality is incomplete

[BryanFauble]

This function is incomplete, more work to support all functionality from the existing synapse class .store() function is needed

[BryanFauble]

This was a hack to make sure that storing files/folders attached to the project and folder class could still be saved. See the logic for annotations and activity is commented out in this code.