(I will add more details later, am in a hurry, I just want to note that quickly for now)
For example when upgrading godot-cpp using bdep sync , we end up with an error about the directory of godot-cpp in the build config directory still alive, and a suggestion to pkg-purge (which is unclear because we used bdep and not bpkg).
The source of the issue seems to be the directory that is generated by python when running the code-generation scripts, the directory and it's content is not tracked by build2.
I can see several ways to fix that but I am wondering of the general issue of having side-effects files generated which are not tracked by build2 and might not be possible to know in advance.
My quick workaround for now is just to recreate the build config, but it's kind of a bazooka approach.