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Jira Server V8.20.8
We had an issue recently where Jira failed to load on a restart - it was not loading many of the core plugins.
One of the workarounds we tried, which seems to have helped, was to delete the Jira plugin caches, i.e. the directories:
<JIRA-HOME>/plugins/.bundled-plugins
and
<JIRA-HOME>/plugins/.osgi-plugins
Is there any potential harm in doing this every time we stop and start Jira?
No clearing the plugin caches will do no harm. Atlassian will even recommend doing this in some cases when you ask for their support.
In my personal experience clearing those caches is often (but not always) required after upgrades of Jira.
Doing this on every Jira restart should not be necessary but if it helps in your case, why not...
Note: the startup of Jira will be slower when the caches are empty
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