Apparently, it is possible to pass different properties for each execution in the `maven-assembly-plugin` as following:
<build>
<plugins>
<plugin>
<artifactId>maven-assembly-plugin</artifactId>
<configuration>
<appendAssemblyId>false</appendAssemblyId>
<descriptors>
<descriptor>src/main/assembly/assembly.xml</descriptor>
</descriptors>
</configuration>
<executions>
<execution>
<id>configuration-staging</id>
<phase>package</phase>
<goals>
<goal>single</goal>
</goals>
<configuration>
<finalName>staging</finalName>
<filters>
<filter>src/main/assembly/staging.properties</filter>
</filters>
</configuration>
</execution>
<execution>
<id>configuration-production</id>
<phase>package</phase>
<goals>
<goal>single</goal>
</goals>
<configuration>
<finalName>production</finalName>
<filters>
<filter>src/main/assembly/production.properties</filter>
</filters>
</configuration>
</execution>
</executions>
</plugin>
Although this does not answer the generic question, it answers the question specifically for `maven-assembly-plugin`.
What a mess. I don't remember where I found this but I had to add the following to get M2Eclipse to be happy. Even more sad is that it isn't exactly easy to understand why this tag is needed.
<!-- language: xml -->
<build>
... various plugins ...
<pluginManagement>
<plugins>
<!--This plugin's configuration is used to store Eclipse
m2e settings only. It has no influence on the Maven build itself. -->
<plugin>
<groupId>org.eclipse.m2e</groupId>
<artifactId>lifecycle-mapping</artifactId>
<version>1.0.0</version>
<configuration>
<lifecycleMappingMetadata>
<pluginExecutions>
<pluginExecution>
<pluginExecutionFilter>
<groupId>org.codehaus.mojo</groupId>
<artifactId>aspectj-maven-plugin</artifactId>
<versionRange>[1.0,)</versionRange>
<goals>
<goal>test-compile</goal>
<goal>compile</goal>
</goals>
</pluginExecutionFilter>
<action>
<execute />
</action>
</pluginExecution>
</pluginExecutions>
</lifecycleMappingMetadata>
</configuration>
</plugin>
</plugins>
</pluginManagement>
</build>
There were a number of other issues with the M2Eclipse plug-in that simply didn't work with Spring Data. In the end I disabled M2Eclipse in favor of the [Apache Eclipse plug-in][1].
[1]: http://maven.apache.org/plugins/maven-eclipse-plugin/
