dumpDifferences and various other improvements
* New utility dumpDifferences reports on differences between two taxonomy versions
* Add code to Flag.java for parsing and printing flags
* Fix bug in setName
* Propagate flag inheritance on taxonomy input
* New utility Taxonomy.maybeTaxon() - no warning if taxon missing
* Taxonomy fixes
    * Further attempts to fix the Trichoderma / Hypocrea situation
    * Deal with triple homonym in NCBI for Trichosporon
    * Tweaks to various synonymies
Tweaks: viruses as a division, empty flags
Repaired bugs introduced in revamping parseFlags and
cycle detection in input taxonomies
Treat a "not found" parent as a root