Hi,
after about a year, I also have the same problem with Geoserver 2.10
installed on Ubuntu 16 (with Tomcat 8): I can only see SpatiaLite (JNDI) and
not SpatiaLite WareHouse.

I downloaded the spatialite plugin from
http://ares.boundlessgeo.com/geoserver/2.10.x/community-latest/
and then I extracted the contents of the archive(2 .jar files)  into the
WEB-INF/lib directory of the GeoServer installation.

I also tried to install the native library for Java (GEOS and PROJ) in the
"user/local/lib" folder. But it's the same: I always see only SpatiaLite
(JNDI) item.

Any ideas about the solution? 

Best regards
Nino



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