resolve annotation row element parsing ambiguity in annotation file (annotationFile)

Up to and including Jalview 2.4, the annotation file format does not support all the annotation visualization representations that Jalview can provide (see related issues regarding stockholm format).

In addition, the documentation (element is differs from the actual annotation format behaviour, and the annotation parser does not conform to the annotation emitter with regard to annotated bargraphs and secondary structure rows.

Procedure for resolution:
1. attach test cases to this bug for data import, output(1), import and output(2) that validate when (1) == (2).
2. Resolve documentation and parser issue (fix emitter and parser to match documentation ?)
3. announce to mailing list and call for people to test their own annotation file examples to make sure the update works.