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>
Update license headers

This trick was performed by:

	mvn license:update-file-header

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
Add a META-INF/ combiner for uber .jar convenience

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

When using @see, you do not need (and should not use) @link too.

Better to just use @deprecated and then @link to the new place.