Fix eclipse project
Clarify sections
Add override or remove methods
Fix warnings by removing unused methods and fields
Deprecate seemingly unused public method
Convert XXX markers to ignoreYYY methods

There were a variety of styles of "TODO" markers for
methods that were not implemented: "TODO not in Model",
"unsupported", etc. This converts all of them to use
helper methods `protected ignoreX()` which log at various
levels. It should be fairly easy now to do a "Open call
hierarchy" style search and see which methods fall into
which category.

Also, **with this commit, the remaining TODOs in the file are valid!**
Other minor cleanups of unneeded XXX type markers, etc.
Fix seemingly broken implementation methods

Unlike the methods which now log with `ignoreY()`, these
methods seem to have been improperly implemented or left
improperly unimplemented. These need careful review.
Merge pull request #3 from joshmoore/extra-annotations

General cleanup of TODO markers and addition of logging