Move app.setupUpgradeHandlers() after module manager and configurator (backport #884)

[mergify]

This is an automatic backport of pull request #884 done by Mergify.

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[codecov-commenter]

Codecov Report

Merging #885 (0ef2203) into v6.x (3bf63f1) will not change coverage.
The diff coverage is n/a.

@@           Coverage Diff           @@
##             v6.x     #885   +/-   ##
=======================================
  Coverage   19.06%   19.06%           
=======================================
  Files         167      167           
  Lines       23684    23684           
=======================================
  Hits         4516     4516           
  Misses      18387    18387           
  Partials      781      781           

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