When loading a manifest file, e.g. by include(), it will chdir first to the
directory of that manifest. This means that all file operations within a
manifest are relative to that manifest's location.
As a consequence of this, additional environment variables are needed to
find absolute paths, so the following are added: $(MPY_LIB_DIR),
$(PORT_DIR), $(BOARD_DIR). And rename $(MPY) to $(MPY_DIR) to be
consistent.
Existing manifests are updated to match.
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