[docs] Fix some javadoc issues #690
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This does clear the main javadoc issues. There are some bug fixes here and only where javadoc plugin complained to fill in rest of required data on existing javadocs. This is significantly smaller than original attempt where I had just added docs for everything. This also does not fix the submodule doc issues but there are far less of those and they can come in later so this is kept to a minimum as needed. Given there is one deprecated item in here, we may want to further consider removing it now but filled it out anyways.