Hmm, I just did a clean checkout from anonymous cvs and the patch
still applied cleanly for me.  Since it sounds like Michael will
make the change in cvs shortly, it's not worth much effort to get
the patch working.  You could make the changes yourself, if so
inclined, with the following command in vi for the five affected
files:

%s/\[\([^\]]\+\)\]\[\([^\]]\+\)\]/(\1,\2)/g

which gets almost all of them - I wasn't dedicated (or skilled?)
enough to come up with a regex that handled cases where a matrix
or array/vector reference is the index for another matrix.
i.e. you'll still have manually to find things like:

  Dur[TotalNotes[v]][v]

and replace them with things like:

  Dur(TotalNotes[v],v)

Anyway I'm getting much too compulsive now, so I'm going to stop.

Russell