This appears to be no longer a issue, if I follow the steps outlined above I
get:
$ click list --manifest
** (process:19378): WARNING **: user.vala:724: com.ubuntu.calculator 1.3.237
does not exist in any database
[]
which sounds entirely reasonable to me. Please let me know if there is
more to do or if I can close this bug.
** Changed in: click (Ubuntu)
Status: Triaged => Incomplete
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https://bugs.launchpad.net/bugs/1225023
Title:
Manually removing packages without removing user symlinks causes chaos
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