Je to napsáno v manuálu apt-mark (man apt-mark):
auto
auto is used to mark a package as being automatically installed,
which will cause the package to be removed when no more manually
installed packages depend on this package.
manual
manual is used to mark a package as being manually installed, which
will prevent the package from being automatically removed if no
other packages depend on it.
hold
hold is used to mark a package as held back, which will prevent the
package from being automatically installed, upgraded or removed.
The command is only a wrapper around dpkg --set-selections and the
state is therefore maintained by dpkg(1) and not affected by the
--file option.