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I don't think Fleet has a Git submodule to process remote targets. Kustomzie is treated a second class citizen in Fleet right now. I wanted to do exactly what you are doing several months ago, asked here and came to the same conclusion. You can use kustomize, but it's all got to be in the same git repo. We ended up putting similar projects based on LoB, team, or audit strategy (some are SOC 1 or 2 apps), and then point fleet at that repo, specify the folder for each app.