CombineAnnotations: support combining legacy annotation indexes, too

Instead of reading all the JSON-formatted indexes ourselves, we can simply
ask the Index class to get all of them for us, including the legacy
annotation indexes, and then write them out using the existing
infrastructure.

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
CombineAnnotations: make the output directory overrideable

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
CombineAnnotations: use the current Thread's context class loader

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
Move CombineAnnotations into the appropriate package

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>