One reminder from the latest meeting: most IDEs will work on the assumption that copying/removing things to "deploy" directories should just work (i.e. no indicator files). So altering that model will break them.
In general, the fileystem hot-deployment API seems to be rmore elevant to IDEs/development, so as Max suggested, correctness is less important than convenience and speed of development.
I don't know, maybe we could offer an option to have 2 implementations, the old style with its problems, and the new "safe" one.