Mark in-active files as fully read before skipping them

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This PR fixes #288

Note that this is missing a unit test to check if consecutive runs with the settings described in the issue properly halt. Sadly I am not sure how to properly check for logstash execution halt within a timeout and as such did not write the unit test myself.

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sincdb clean up test failure suspected to be unrelated to the code changes of this PR. I am unable to find the cause of the problem also see #287 which encounters the same failures.