For a search engine that will be used on lots of little sites, is there any downside to having a lot of apps, and linking to generic pipeline objects? They want to have site-specific synonyms and spelling suggestions.
Lucidworks Fusion - lots of apps OK?
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If by "lots" you mean a few dozen then you are likely fine. Once a cluster gets around 1000 collections, Zookeeper can't keep up with needed coordination tasks and each app will likely have several collections.