Prefer signed types, and remove -Wall -Wextra warnings

[andresy]

Proposed changes

• array class prefers int64_t instead of size_t
• SmallVector is inherently small -- sizes are now int
• propagate the signedness through the codebase and fix warnings accordingly

Checklist

Put an x in the boxes that apply.

• [x] I have read the CONTRIBUTING document
• [x] I have run pre-commit run --all-files to format my code / installed pre-commit prior to committing changes
• [x] I have added tests that prove my fix is effective or that my feature works
• [x] I have updated the necessary documentation (if needed)