By selecting command “Upgrade” from the command search, and then selecting “Refresh Listing”, all upgraded plugins shown version “1.0”, status “orphan” and column “Name” displayed short name instead of the full name, such as “scm” instead of “Source Control Management”. At the same time, these plugins with full names existed in the same list with status “available” and latest fetched version string.
Orphaned plugins disappeared after manually selecting “Install” on every such plugin.