Add documentation to newly implemented `Context` class and `StorageManager`

[ethanholz]

Related to #690. This issue will be used to track what things we might want to scope for documentation on the new Context architecture. So far, I have the following list of things that need to be covered:

• gufe ExternalStorage and how it is used
• How we use ExternalStorage in the new Context class and affiliated assumptions
• How one might migrate a protocol to use this new paradigm

[ethanholz]

Pinging @atravitz for context if there is scope I am missing in writing these docs.

[atravitz]

Yes this sounds good! I think being super clear about scratch, shared, permanent and what behavior is built in. Also being specific about how interrupted/failed runs are handled.