viz changing apt: this was already proposed (and rejected) at
DOXIA-47. Even though we are now discussing changes to the original apt format (http://docs.codehaus.org/display/DOXIA/Proposed+Changes+to+the+APT+Format) I'm not in favor of this particular change, because it's not motivated by a necessary bug fix or missing feature. IMO we risk more by confusing users and breaking things than we gain by a more intuitive behavior.
viz. xhtml sink: there is an issue to discuss I think, eg I don't see why one should be forced to use href="./other.html" instead of just href="other.html" in an xdoc document (in apt you have to because there is no other way to distinguish internal from external links).
I think we can easily define how parsers should emit link events link( String name ) : if name starts with # it's an internal link and the receiving sink can decide what to do with it. The StructureSink.isExternalLink method is apt specific, it should not be used by other sinks.