Hello,

I am not familiar with JNDI configuration, but the path '[tomcat-home]/conf/Catalina/localhost' is the path to the deployment descriptors,
so each file under the path defines an application to be deployed to the server.
IDEA copies Tomcat configuration (and possibly modifies the copy) on each start of the run configuration.
The '[tomcat-home]/conf/Catalina/localhost' folder of the copy is cleared by default.
Since you don't need to clean the folder copy, you should just check the 'Deploy applications configured in Tomcat instance' in the IDEA Tomcat run configuration.

Alternatively – as I can see from docs (http://tomcat.apache.org/tomcat-5.5-doc/jndi-resources-howto.html), but haven't tried it myself – you may configure JNDI with:

• <application root>/META-INF/context.xml
  
• <application root>/META-INF/web.xml
  
• [tomcat-home]/conf/server.xml

Also, there were no relevant changes in IDEA Tomcat support since 11 release, so I suspect you've just lost the value of 'Deploy applications configured in Tomcat instance' checkbox somehow.

Regards,
Michael