THtml now copes with the new directory structure - in fact it can now support any directory structure: users can implement their own definition of libraries, of where to find sources and how headers are included by means of traits-like objects. See THtml::THelperBase for their common base; the derived classes implement customizable functionality.
Some small improvements are THtml's improved Search field in the top box of every page, and the display of methods' signal / menu / etc setting (the new yellow labels in the list of function members). Templates mentioned e.g. in sources or comments now get linked. All generated pages now show the date of the last source modification and the date when the HTML page was last generated.
THtml now also documents typedefs to classes on a separate page. This is useful for e.g. TMatrixD, THnSparseF, etc where users might not realize that it is a typedef. Now the page states that it's a typedef and forwards to the documentation of the underlying class.