DL4J Layer etc autogen docs polishing

Let's consider a simple example: DenseLayer
https://deeplearning4j.org/docs/latest/deeplearning4j-nn-layers

Some issues here:
1. "If true (default): include bias parameters in the model. False: no bias." - no context here (it's doc from "hasBias" method - but nothing to signify that)
2. None of the inherited methods are listed there (so we're missing 95% of the configuration options for DenseLayer as a result)
3. The class javadoc (which admittedly isn't great anyway) isn't included: https://github.com/deeplearning4j/deeplearning4j/blob/451dd76b50355358dc176f2b704e98c43423c5b8/deeplearning4j/deeplearning4j-nn/src/main/java/org/deeplearning4j/nn/conf/layers/DenseLayer.java#L33

Some other general suggestions and issues. Some of these will have to be fixed at the javadoc level.
1. A 1-line link at the top of these autogen pages (to each layer etc) would make them easier to navigate
2. Deprecated methods are included in some layers (Like: "activation" method under General layers). IMO exclude deprecated.
3. It might be good to make the layer configuration options collapseable, and collapsed by default (i.e., click to show). Probably too much content otherwise.
4. Some of our javadocs have links but not actually in HTML format, and don't render as actual clickable links in the website docs. Should we detect these and fix that? (Alternatively, let's fix it in the javadoc). Example: Yolo2OutputLayer - https://github.com/deeplearning4j/deeplearning4j/blob/master/deeplearning4j/deeplearning4j-nn/src/main/java/org/deeplearning4j/nn/conf/layers/objdetect/Yolo2OutputLayer.java
5. If we are doing links to source for each version, shouldn't we be linking at a specific commit ID, and not to master? Otherwise I could be browsing 1.0.0-beta2 docs, click on the link, and see completely different content than I expect (due to changes since the release)
6. There's some random stuff, like setBackpropGradientsViewArray under ReverseTimeSeriesVertex - https://deeplearning4j.org/docs/v1.0.0-beta2/deeplearning4j-nn-vertices - perhaps listed here due to lack of an ```@Override``` annotation
7. I don't believe that Javadoc class links work - it'd be awesome (but no doubt hard) to have stuff like this work as a link: ```{@link org.deeplearning4j.nn.weights.WeightInit#NORMAL}```
8. Let's include any public enumerations? (I don't think this is done currently?)