Increment the project version from 0.3.0 to 0.3.1 in mix.exs and documentation.
This release focuses on upgrading core and test dependencies to their latest
compatible versions.

Key changes:
- Update version to 0.3.1 in mix.exs and README.md
- Upgrade crucible_ir from ~> 0.1.1 to ~> 0.2.1
- Upgrade supertester from ~> 0.3.1 to ~> 0.4.0
- Update mix.lock to reflect new dependency versions
- Add release notes and update comparison links in CHANGELOG.md