There wouldn't have been a problem in any case if the GPL parts of the
code had been clearly marked and accompanied by their license. Then the
license could be removed once all the covered code is gone, and in the
meantime the work in progress is in compliance.
If it's the developer's intention to replace all the GPLed code
eventually, then it seems to me that clearly marking it is a necessary
step. But that didn't happen.
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