There's probably, in spirit, a graph version of the BWT, but I'm not familiar enough to know it. The approach is less straightforward because you're not just modifying BWT to allow for indels/errors, but rather a graph compression algorithm to allow for fragment searching along vertices of a sequence graph. That said, it has to happen eventually. It's been a while since I took comp bio (sequences & graphs) but what you mentioned is what I learned (and I took it from Waterman, so what I'm saying is that I think you've got it).

You can look at Pall's work to see how the current approaches may evolve into something compressible:

https://github.com/GFA-spec/GFA-spec

As far as articles? McVean's, without a doubt!

http://www.nature.com/ng/journal/v47/n6/full/ng.3257.html

An implementation paper for graph assembly HLA typing is at:

http://biorxiv.org/content/early/2015/12/24/035253

Interesting times ahead, with people recognizing that GxE and GxExE matters far more than G alone.