Refactor permutation and sequence distance interfaces and classes

[cicirello]

Summary

Refactored interfaces related to permutation distances into a hierarchy, refactored interfaces related to sequence distances into a hierarchy, eliminated a couple package-private abstract classes after moving methods into appropriate interfaces as defaults.

Closing Issues

Closes #116 and Closes #117

Types of changes

• Bug fix (non-breaking change which fixes an issue)
• New feature (non-breaking change which adds functionality)
• Breaking change (fix or feature that would cause existing functionality to change)
• I have read the CONTRIBUTING document.
• My code follows the code style of this project.
• My change requires a change to the documentation.
• I have updated the documentation accordingly.
• I have added tests to cover my changes.
• All new and existing tests passed.
• I edited the Unreleased section of the CHANGELOG.md with any relevant bullets.