program.copy() is shallow

[bramathon]

Pre-Request Checklist

• [x] I am running the latest versions of pyQuil and the Forest SDK
• [x] I checked to make sure that this feature has not already been requested

Issue Description

The .copy() method on a pyquil program is shallow, which can cause suprising behaviour from users who expect it to be deep.

Proposed Solution

Make it a deep copy.

Additional References