Logback 2 (incl. docs)

As a follow-on to #889, this PR makes further going (and likely harder to check) changes. The goal is to hide references to loci_tools.jar where possible and where not to clearly include the new package name beside references to loci_tools.jar. The goal: minimum confusement.

Code testing points for @pwalczysko:
 * The bftools.zip should contain `bioformats_package.jar`
 * The updater functionality (Plugins > LOCI > ...) should download `bioformats_package.jar`  and not `loci_tools.jar`