@Andrew at the risk of stating the obvious are none of the following practical?
1) uninstall the store version
2) name your test app something else
3) version the test app to be newer
4) don't get updates while actively developing

** No longer affects: canonical-devices-system-image

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https://bugs.launchpad.net/bugs/1513860

Title:
  'Latest' version of a click package used after reboot

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