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Flex Application (SWF files) are usually run on web context (WAR project). So is necessary to copy SWF files (and all runtime dependencies) into the WAR during packing phase. That is exactly what copy-flex-resources goal does.

<build>
...
  <plugins>
  ...
    <plugin>
      <groupId>org.sonatype.flexmojos</groupId>
      <artifactId>flexmojos-maven-plugin</artifactId>
      <executions>
        <execution>
          <goals>
            <goal>copy-flex-resources</goal>
          </goals>
        </execution>
      </executions>
    </plugin>
  </plugins>
</build>

Then, is necessary to add a dependency to all SWF. Like this:

...
  <dependencies>
    <dependency>
      <groupId>org.sonatype</groupId>
      <artifactId>swf-project</artifactId>
      <version>1.0</version>
      <type>swf</type>
    </dependency>
  </dependencies>

Do not forget to declare type as swf.

What this goal does:

1. copy all dependencies type SWF declared on project.
2. copy any RSLs required by SWF (don't forget to generate optimized libraries on each SWC)
3. copy runtime locales (only when the project is compiled by flexmojos and uses runtimeLocales configuration)