Further refinements:

1. Fading and unfading of the notes dif on the right of the text, which was broken by the new apparatus code, is now fixed.
2. Interaction with the apparatus area now automatically unfades and unhighlights all areas above, so the main text area returns to its normal settings.
3. Highlighting of the lemma in the popped-up line has now been refined somewhat. Where the whole line is the lemma, no highlighting is done, because it's pointless. Similarly, where there are multiple instances of the lemma in the line, no hightlighting is done, because only one of the highlights would be the right one, and the code cannot know which (see discussion below).
4. I tweaked the page layout so that the popup line appears to the right of the apparatus, and does not obscure it.

This issue of highlighting lemmas could use some input from Ray and Cara. Take the example of LDev003 line 8:

do displease the not tho I do reffreyn

One reading shows this:

8 do] omit. LDev145, AAH06, LEge20, STC13860_12.

Now, "do" appears twice in the line, so it's not clear from the apparatus which "do" is omitted here. We might be confident that readers may decide correctly for themselves (although I can't; the line seems OK with either "do" missing), but it's not ideal. I think a better solution would be to intercept these instances and rewrite them like this:

8 do displease] displease LDev145, AAH06, LEge20, STC13860_12.

(assuming that the first instance of "do" is the one omitted.) This would make it clear which "do" is dropped, and in the process it would disambiguate the reading from the point of view of the processing code, so that I could confidently highlight "do displease" when popping up the line.