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Can metapackage directory contain the package files?
No. Metapackages should be empty. See #q256493 for a discussion of what metapackages are used for.
Moreover can I refer metapackage in rosrun e.g. rosrun metapackage node.
No. Metapackages do not contain any executable artefacts, so you cannot use them with rosrun
.
See REP-140 - Package Manifest Format Two Specification - Data Representation - <metapackage/> (also referenced in #q256493) for the normative text that defines what metapackages are, what their structure/layout/contents is and why they are used.