First of all perform reindex only when you have to. There is no need to do it regularly.
You can trigger reindex from REST API: https://docs.atlassian.com/jira/REST/server/#api/2/reindex-reindex
It's always worth questioning why you want to do this. There are some cases where it makes sense, but if you're doing it because your index is regularly going wrong, then this is absolutely the wrong thing to do.
There's a phrase "plastering over the cracks" - when your house is structurally unsound, cracks appear in the plaster as it gradually falls apart. If you "plaster over the cracks", your house might look ok to the eye, but you're hiding the fact that it's going to fall down soon.
So, if you're doing this because you're getting indexing errors a lot, you need to fix that, not pretend you don't have a massive problem.
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