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Fix backward compatibility for old model checkpoints

Jay Chan requested to merge jay_fix_old_ckpt_compatible into dev

This MR fixes the incomplete backward compatibility introduced by the !79 (merged)

Specifically, the old model checkpoints contain the old feature naming scheme which needs to be converted as well. This MR adds the conversion for the checkpoint configs.

In addition, this MR also fixes the incorrect check of the pyg keys which leads to some unnecessary warning message.

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