How do I fix the order of the tracks in an integrated GenomeView instance?

Answer: 

You can fix the order in which the tracks appear in the configuration file that you supply to the GenomeView instance.

Add lines of the following type to the configuration file to have the gene, mRNA and CDS annotation tracks near the top.

track:weight:gene=1
track:weight:mRNA=2
track:weight:CDS=3

The higher the weight, the lower the track will be displayed.

Tracks that do not have an explicit weight set in the configuration file, will receive one starting at 1000.

The structure track and the ruler have weight -1 and -2 respectively, making sure they are always at the top.