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What is the best way to recreate and deploy an app with a custom navigation bar from a 5.0.7 search head in a 6.3.3 search head cluster?

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We currently have a standalone search head (5.0.7) with customization to the nav bar ( etc/apps/search/local/data/ui/nav/default.xml ) to help users quickly access searches and dashboards. We are building a new search head CLUSTER (6.3.3), and I do not know how to recreate this when using the deployer for the cluster. It seems it would be a simple matter of deploying the default search app with our tweaks, but the docs specifically say not to deploy default apps like search. Manually copying the file into the search app on all the cluster nodes seems backwards and would be annoying to keep up to date. What's the best way to solve this?

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