Over a month ago, I had some reports that syncing into adjusted branches
was losing some files that had been committed. I couldn't reproduce it, but
IIRC both felix and tbm reported problems in this area. And, felix kindly
sent me enough of his git repo to hopefully reproduce it the problem.

Finally got back to that today. Luckily, I *was* able to reproduce the bug
using felix's repo. The bug only occurs when there's a change deep in a
tree of an adjusted branch, and not always then. After staring at it for a
couple of hours, I finally found the problem; a modification flag was not
getting propagated in this case, and some changes made deep in the tree
were not getting included into parent trees.

So, I think I've fixed it, but need to look at it some more to be sure, and
develop a test case. And fixing that exposed another bug in the same code.
Gotta run unfortunately, so will finish this tomorrow..

Today's work was sponsored by Riku Voipio.
