Comment cleanups to improve generated docs

- added comments to fields which didn't have any.
- changed all `//` comments to the new format
- fixed indents/line lengths/style on lines I touched
The mapping quality is not about the matches and indels in the alignment, but rather about how confident you can be in the read mapping here in the genome rather than somewhere else, i.e. how much better the alignment in this location is than all the other candidates elsewhere in the genome.  Perhaps use text:

  /** Represents how confident we are that the read maps to this place in the referenceSet as opposed to other locations. */

On 15 Jul 2014, at 22:37, Frank Austin Nothaft <notifications@github.com> wrote:

> In src/main/resources/avro/reads.avdl:
> 
> >      union { null, int } mappingQuality = null;
> > +
> > +    /** Represents how well this alignment maps to the reference. */
> Isn't this more Represents the local alignment (alignment matches, indels) versus the reference?
> 
> —
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