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Issue is related to arduino/arduino-pro-ide#416
I deduced that the call for file listing issued by the IDE over gRPC gets the CLI to recursively go through the tree hence returning every file.
This creates the issue linked above.
For how the Sketch is structured, there should be no recursion, and only files at the main Sketch level should be returned.
Environment
CLI version (output of arduino-cli version): 0.15.x