Index pattern automatic refresh - move to migration step

[mattkime]

Index patterns will automatically refresh if any field in the field list is missing certain attributes. If the user doesn't have permissions to do this they will see an error. This behavior can be frustrating and is surprising to developers - #65284

We should

a) Make sure no code in the stack is writing index patterns that trigger a refresh.
b) Migrate index patterns that need updating
c) Update index pattern fields on a field by field basis instead of recreating the field list. This may prevent fields from being revealed that are hidden due to security privledges.

[elasticmachine]

Pinging @elastic/kibana-app-arch (Team:AppArch)

[mattkime]

no longer relevant due to removal of field cache - #78758