upgrade from 4.0.1 to 4.1.4 is removing the system files

[Joseph D. Edwards]

Hello again.

idp 4.0.1 to 4.1.4

we reviewed and followed:
https://shibboleth.atlassian.net/wiki/spaces/IDP4/pages/1265631513/Upgrading,
https://shibboleth.atlassian.net/wiki/spaces/IDP4/pages/1265631499/ReleaseNotes,
https://shibboleth.atlassian.net/wiki/spaces/KB/pages/1469908146/Example+4.1+Upgrade

before upgrade
ls system
conf  DONOTTOUCH  flows  messages  views

after upgrade
ls system
conf DONOTTOUCH

Any hints on how to proceed?

Joe, UWMC
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