Here's a patch which fixes these two problems.
Unfortunately Javadoc groups can't be used for contrib modules that have classes in the same packages as core MapReduce (e.g. Mumak which includes classes in o.a.h.mapred), since they are specified on a package basis, rather than a source directory basis. For this reason I have removed these contrib classes from the user Javadoc, but I've left them in the "developer Javadoc" which is generated using the "javadoc-dev" target. This only affected Mumak.
In the long run we can fix this by re-packaging the contrib modules that do this (in addition to Mumak, this includes the scheduler implementations) and use the InterfaceAudience annotation appropriately. (Related to MAPREDUCE-561.)
There are some contrib modules which should have their user Javadoc published. I have opened
MAPREDUCE-1626 to address this problem, since there are lots of warnings that need fixing in doing this.