Having both share the same root is fine. Apache Freemarker Docgen uses this structure. Invoking the JavaScript build from within the Java build is the standard. Running npm install can be decided programmatically by the Java build. For example, in Maven:
<plugin>
<groupId>com.github.eirslett</groupId>
<artifactId>frontend-maven-plugin</artifactId>
<version>0.0.27</version>
<executions>
<execution>
<id>install node and npm</id>
<goals>
<goal>install-node-and-npm</goal>
</goals>
<configuration>
<nodeVersion>v4.2.1</nodeVersion>
<npmVersion>3.5.3</npmVersion>
</configuration>
</execution>
<execution>
<id>npm install</id>
<goals>
<goal>npm</goal>
</goals>
<configuration>
<arguments>install</arguments>
</configuration>
</execution>
<execution>
<id>npm run build</id>
<goals>
<goal>npm</goal>
</goals>
<configuration>
<arguments>run build</arguments>
</configuration>
</execution>
</executions>
</plugin>
References