Certain files set to "transparent" using aemt are not handled correctly at the integration stage. In particular, if config files are made transparent, they vanish from the integration directory, making progress impossible.
Furthermore, if a file is made transparent after being modified in the grandparent branch, it is also deleted from the integration directory, so when the parent branch is integrated, the file is no longer in the baseline (although it is still recognized as a project file).
The attached test illustrates the problem.
Priority should be low, since the work-arounds are fairly obvious, if tedious.
Applies to 4.23.D430