I just started using the assistant on an existing annex. I fire up the assistant like so:

$ git annex webapp

Everything syncs and looks to be working fine. In another terminal, I then create a new file:

$ touch testfile.txt

The assistant sees that file, immediately adds it and syncs. Ok. So now I want to edit that file.

$ git annex unlock testfile.txt

As soon as I unlock the file, the assistant re-adds it to the annex and syncs, preventing me from editing the file. How can I edit files with the assistant running?