Replicate the issue by loading into Pharo (I’m using 4) with:

Metacello new
baseline: ‘Pillar’;
repository: ‘github://JupiterSmalltalk/Pillar/repository';
load.

Then evaluate:

PRPillarGemstoneCodeTool port

At this point, the methods and variables that were in the trait, appear to be in the 4 classes that used the trait, however, monticello doesn’t see them as changes so doesn’t write them to the filetree.

You'll see that the PRPillarGemstoneCodeTool ->#port method simply flattens traits, removes them, then recompiles the methods in the classes that had traits.