Where in maven project's path should I put configuration files that are not considered resources

The question is what is the best solution of the two? If the correct is 2, what is the best way to copy it to target folder? Is there any other solution better and more common than those two?

Since you want that file to be copied to the target/classes folder, it has somehow to be considered as a resource (so either put in under src/main/resources or declare src/main/conf as resource directory). And if you don't want it in the final jar, configure the Maven JAR Plugin to exclude it:

<project>
  ...
  <build>
    <plugins>
      ...
      <plugin>
        <groupId>org.apache.maven.plugins</groupId>
        <artifactId>maven-jar-plugin</artifactId>
        <version>2.3.1</version>
        <configuration>
          <excludes>
            <exclude>**/conf/*</exclude>
          </excludes>
        </configuration>
      </plugin>
      ...
    </plugins>
  </build>
  ...
</project>

For the assembly part, assembly descriptors are pretty flexible so it should be possible to achieve what you want regardless of the choice. I'd suggest using the easiest setup though.

My solution was to use two profiles: Development (default) and Packaging

My default / section contains both src/main/resources and src/main/conf. I call this my Development profile, which is an implicit profile.

My packaging profile is an explicit profile which is defined under section. There under / I only mentioned src/main/resources. When I'm running my packaging script (we currently have this external to maven since its building an RPM out of our WAR), I'm running 'mvn install -Drpm' to activate my Packaging profile (rpm is the id for the Packaging profile.

If this wasn't clear enough, feel free to ask more questions.