Support path kind changing without delete and add pairs

Every path in a tree has a kind - directory, file or symlink. Its possible for a user to change the kind of a path without doing a logical delete + add. I.e. they might change a file called 'doc' which was a symlink into a directory called 'doc'. Or a regular file might be turned into a symlink if its content was adsorbed into an existing file but they needed the path kept for compatability.

We should stop giving errors when these changes occur and instead record the actual tree correctly. We may need to increase our testing and or merging logic to accomodate corner cases we currently punt on which become possible with this in place.