The complexity and medium-specificity of all this just shows that computer-based annotations (considered as semi-permanent artifacts) aren't worth the trouble.

The complexity and medium-specificity of all this just shows that computer-based annotations (considered as semi-permanent artifacts) aren't worth the trouble. Our systems aren't ready for them, and will only become so when we have some kind of interoperable standardised protocols or data formats. Possibly never, but certainly not now. Until our systems have reached some sort of maturity (not guaranteed of course), consider annotations as transient, and if an ongoing artifact is needed, incorporate them into notes or papers or whatever in your long-term format of choice.