There are a couple reasons to move on from/fork therapi, discussed in (and then copied here from) scijava/incubator#28:

1. Therapi is an source-time annotation processor. It might have access to the parameter names of methods, even though they are typically not stored into the bytecode. If so, we could map the @param names to the actual parameter names, in case the @param declarations are out of order, or some are missing, or some are spurious. This would be better than the current assumption that everything is there, and in same order as the method.
2. In the case of mixed @param and @input/@output, therapi indexes things in such a way that the order is lost. We should consider either:

• Submitting an issue and/or PR to therapi adding a general-purpose getter of all the javadoc annotations in original order; or
• Fork therapi and merge its logic into scijava-indexer, so that everyone can have this functionality without incurring additional annotation-time dependencies.