Make repair command more flexible

[matentzn]

Resolves #1099, and makes repair command more flexible.

• [X] docs/ have been added/updated
• [X] tests have been added/updated
• [X] mvn verify says all tests pass
• [ ] mvn site says all JavaDocs correct
• [x] CHANGELOG.md has been updated

This PR makes it possible to selectively invoke repair functions rather than having all or nothing approach (which still works by default).

WARNING: This PR contains a breaking change:

robot repair --input in.owl --merge-axiom-annotations true -o out.owl

would have previously ran the entire repair pipeline (RepairOperation.repair()). Now, it will only run the merge axiom annotations pipeline.