Always modify packages.common in gen-tarball.sh

* packages/gen-tarball.sh (update): Fix removal of old
package.
* pacakges/gen-tarball.sh: Always replace the package
in packages.common

This also always prints out the snippet regardless of
uploading the package. Always modifying the packages
list seems logical and resolves the problem that --auto
did both upload and modifiy.

Always modifying the packages.common seems logical and
more transparent even when developing to distinguish failed
downloads and intentional use of snapshots.