Remove prune flag as an external API

[carver]

It's too easy to screw up handling of pruning when you use it directly. We should direct everyone to use the squash_changes() API instead. Let's remove the prune keyword from init, and add some internal-only API to enable pruning from within squash_changes.

It seems this needs to go into a major version bump

It's possible that we might be able to hide away the prune keyword somehow and force squash_changes as the only approach to do that. I think we could cover both use cases that way, but I'm not sure how it would look to launch a pruning trie from inside squash_changes() (which uses the prune keyword internally right now).

Originally posted by @carver in #93 (comment)