write auto-bits before calling dpkg & again after if needed

Writing first means that even in the event of a power-failure the
autobit is saved for future processing instead of "forgotten" so that
the package is treated as manually installed.

In some cases we have to re-run the writing after dpkg is done through
as dpkg can let packages disappear and in such cases apt will move
autobits around (or in that case non-autobits) which we need to store.

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