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The error is happening because checkout runs inside the newly cloned directory. So the clone method could be changed to resolve the restart path before passing the path to checkout. The code documentation will need to be fixed too.
Doing a payu clone using a relative restart path doesn't work with a warning:
As it relies on an absolute path
https://github.com/payu-org/payu/blob/master/payu/branch.py#L245-L246
This could be clearer in the docs and help, e.g.:
its also not clear to me why the relative path can't work?
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