Individual context can be defined in individual files (with a ".xml" extension) in the $CATALINA_HOME/conf/[enginename]/[hostname]/ directory. The name of the file (less the .xml) extension will be used as the context path. Multi-level context paths may be defined using #, e.g. foo#bar.xml for a context path of /foo/bar. The default web application may be defined by using a file called ROOT.xml.
WARNING [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployDescriptor A docBase /usr/local/tomcat/webapps/mywebapp inside the host appBase has been specified, and will be ignored
The TOMCAT_HOME/conf/Catalina/localhost directory is one of the recommended places to put Context xml files, but the problem with the root context is that normally the context file's name determines what the Tomcat webapp context path will be. And that, incidentally, overrides the context path defined within the context XML file. One of Tomcat's quirks
Your best bet to get what you want would be do delete the TOMCAT_HOME/webapps/ROOT directory contents and replace it with your own webapp
I should note that any static items specific to the Java webapp should be part of the Java webapp. Having Apache serve them separately stopped being more efficient about 15 years ago.