Use 'true' ids and sequence ref when storing annotation in project

<Annotation> element in project uses AlignmentAnnotation.id (which is hashCode()).
This is theoretically not unique. A simple reference counter ann0, ann1, ann2,... would be safer.

Annotation sequenceRef attribute is set to sequence name - not guaranteed unique.
As per comment in the code at storeAlignmentAnnotation, would be better to use sequence (XML) id.
This is available in the seqsToIds lookup table.
Similarly on load, the seqRefIds reverse lookup can provide the sequence.
If this change is made, project load would need to still handle sequence lookup by name as a fallback, for backwards compatibility.