Sequence Ontology functional annotation doc fixes

I have added links to the Sequence Ontology MISO browser for all the SO terms used in the functional annotation documentation.

In doing so I found a few errors (e.g. feature elongation should be feature_elongation, non_coding_exon_variant should be non_coding_transcript_exon_variant) and at least one term that I could not correct (nc_transcript_variant).

I haven't looked at the GEMINI code yet to see if the same corrections need to be made there, or if these were just documentation errors.