The Patch Plugin can be configured to apply sets of patches from multiple directories. In the example below, the plugin is setup to apply all the patches in a bugfix directory with optimization (will not reapply the same patch) and also from an enhancement directory. This scenario might crop up if you don't have commit access to a project's source yet need to apply bugfix and enhancement patches. The two different patch source directories are shown purely as an example of what can be configured.
<project>
[...]
<build>
[...]
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-patch-plugin</artifactId>
<version>1.2</version>
<configuration>
<targetDirectory>${moduleDirectory}</targetDirectory>
<skipApplication>false</skipApplication>
</configuration>
<executions>
<execution>
<id>bugfix-patches</id>
<configuration>
<patchDirectory>src/main/patches/bugfix</patchDirectory>
<patchTrackingFile>${project.build.directory}/optimization-files/bugfix/patches-applied.txt</patchTrackingFile>
<naturalOrderProcessing>true</naturalOrderProcessing>
</configuration>
<phase>process-sources</phase>
<goals>
<goal>apply</goal>
</goals>
</execution>
<execution>
<id>enhancement-patches</id>
<configuration>
<patchDirectory>src/main/patches/enhancement</patchDirectory>
<patchTrackingFile>${project.build.directory}/optimization-files/enhancement/patches-applied.txt</patchTrackingFile>
<naturalOrderProcessing>true</naturalOrderProcessing>
</configuration>
<phase>process-sources</phase>
<goals>
<goal>apply</goal>
</goals>
</execution>
</executions>
</plugin>
</plugins>
[...]
</build>
[...]
</project>