Add support for memory references in substitute() method

[mhodson-rigetti]

Description

Addresses #1383 generally as suggested. However, because the identity of a memory reference (as a key- ie. its hash) includes the offset, and substitution is via a map using this key, it was easier to ask the user to address each offset to be substituted individually. Thus, conceptually, the substitution map is { x[0]: <number>, x[1]: <number>, x[2]: <number> } for some array x of length 3.

I'm assuming there are no large-scale performance expectations on this new ability where the array access would make a difference. There is no impact on previous code paths. The alternative would be to use the names (strings) only as the key, but that would technically be a breaking change, where as this PR is not (the key is covariant to the previous Parameter class, and now also MemoryReference).

Checklist

• The PR targets the rc branch (not master).
• Commit messages are prefixed with one of the prefixes outlined in the commit syntax checker (see pattern field).
• The above description motivates these changes.
• There is a unit test that covers these changes.
• All new and existing tests pass locally and on the PR's checks.
• Parameters and return values have type hints with PEP 484 syntax.
• Functions and classes have useful Sphinx-style docstrings.
• All code follows Black style and obeys flake8 conventions.
• (New Feature) The docs have been updated accordingly.
• (Bugfix) The associated issue is referenced above using auto-close keywords.
• The changelog is updated, including author and PR number (@username, Test ignore #1234).