Use Javadocs rather than source code links when possible

See https://trello.com/c/u96Pr1vO/91-bio-formats-general-doc-improvements

--no-rebase
Only advantage of such shortcuts is to simplify links to API methods i.e.

```
:formatreader:`method(type arg1, type arg2)`
```

But if this is overkill, happy to revert to using `javadoc` across the board.