Restored dictionary generation for private sub-classes.

Restored dictionary generation for private sub-classes.
The generation is conditional on the ROOT version used:
If it's less then 5.99 (ROOT6-alpha) then we do generate the
dictionaries.  If not, then the dictionaries are not generated.
Perhaps we need to make the sub-classes public for the up-coming
ROOT6 (May 2014 apparently) if needed for object persistency of
the parent classes.

Fixed up link of runTrain to take LDFLAGS into account.