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PORTSDIR/INDEX-__FreeBSD__.db is usually generated by ports-mgmt/portupgrade
However, you can use the tool 'pver_dbgen' to generate/update it

> sudo pver_dbgen

The tool use PORTSDIR/INDEX-__FreeBSD__ to generate db file

Then you can show the packages whose port version and package version is different
by typing 'pver'
> pver

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