We couldn't start the following plugins:
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Look into {{ jira home }}/log/atlassian-jira.log, when Jira starts, it logs the plugins it's loading. There is a time threshold during which plugins are expected to all start - if one of your plugin occupies that timer then after the threshold plugin loading will stop, which can explain some of your plugins disabled on start up or failing to start Jira at all.
If a plugin fails to load - you will see an error why, if it is loading for too long, you will see it there too.