Replace WFlags with WindowFlags

It has long been in Qt 4 that the WFlags window flags argument has been
renamed to WindowFlags. In fact, WFlags is just a typedef to WindowFlags.
In Qt 5, this will go away, so we can change this now to make transition
easier in the future.

This should not have any affect on API or ABI, as the symbol names already
have WindowFlags in them anyway.

This change concentrates on the sources in the src directory. There are
a few more places in the python directory that can be done later.