Hi — thanks for the thorough analysis and the proposed patch. The fix
was merged as GitHub PR #26 (commit 0a44bf21, 2018-05-27) by Mark Kelly.
The ___update_needed() function now checks three timestamps instead of
two: /var/lib/apt, /var/lib/apt/lists, AND /var/log/dpkg.log (d3). Since
dpkg.log is updated when package operations complete, this correctly
triggers a cache refresh after upgrades finish, eliminating the stale
update count. Additionally, the cache write now uses an atomic write-
then-move to prevent race conditions. Closing as Fix Released.

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https://bugs.launchpad.net/bugs/1604750

Title:
  Byobu not clearing update numbers after updates

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