The application-types.xml along with accompanied files located in src/main/resources/examples directory allow a developer to see the user-defined input/output metadata defined. This helps in understanding how mapping are built. But obviously they are not needed during build or run time. I prefer leaving these files when I source control it, so other developers can see how mappings are built. Add the exclude tag in pom.xml to exclude these files from the final build as follows:
<build>
<resources>
<resource>
<directory>src/main/resources</directory>
<excludes>
<exclude>examples/**</exclude>
<exclude>application-types.xml</exclude>
</excludes>
</resource>
</resources>
...
</build>