I have created a multi-module project with two separate "web" applications - as the project requires two discreet web applications (one for admin and one that is public-facing).

The major change was to duplicate the contents of the web directory created from the archetype - and rename the two web directories as "admin-client" and "public-client". The following lines in the base pom.xml was changed
    <modules>
        <module>core</module>
        <module>web</module>
    </modules>

to:

    <modules>
        <module>core</module>
        <module>admin-client</module>
        <module>public-client</module>
    </modules>

Each of the modular pom.xml were also updated to reflect the naming conventions.

When executing the mvn appfuse:full-source task, it successfully executes for the 'core' module.
However, it fails on the 'admin-client' module:

[INFO] ----------------------------------------------------------------------------
[INFO] Building Application - Admin Web Client (Spring MVC)
[INFO] task-segment: [appfuse:full-source]
[INFO] ----------------------------------------------------------------------------
[INFO] [appfuse:full-source]
[INFO] [AppFuse] Installing source from web-common module...
[INFO] [AppFuse] Installing source from spring module...
[ERROR] Failed to copy jdbc.properties to core module
[INFO] [AppFuse] Source successfully exported, modifying pom.xml...
[INFO] [AppFuse] Removing maven-warpath-plugin...
[INFO] [AppFuse] Adding dependencies from web-common module...
[INFO] [AppFuse] Adding dependencies from spring module...
[INFO] [AppFuse] Removing maven-warpath-plugin...
[INFO] [AppFuse] Updated dependencies in pom.xml...
[ERROR] Unable to write to pom.xml: File 'web/pom.xml' does not exist
java.io.FileNotFoundException: File 'web/pom.xml' does not exist
        at org.apache.commons.io.FileUtils.openInputStream(FileUtils.java:136)
        at org.apache.commons.io.FileUtils.readFileToString(FileUtils.java:961)
        at org.apache.commons.io.FileUtils.readFileToString(FileUtils.java:979)
        at org.appfuse.mojo.installer.InstallSourceMojo.createFullSourcePom(InstallSourceMojo.java:428)
        at org.appfuse.mojo.installer.InstallSourceMojo.execute(InstallSourceMojo.java:277)
        at org.apache.maven.plugin.DefaultPluginManager.executeMojo(DefaultPluginManager.java:443)
        at org.apache.maven.lifecycle.DefaultLifecycleExecutor.executeGoals(DefaultLifecycleExecutor.java:539)
        at org.apache.maven.lifecycle.DefaultLifecycleExecutor.executeStandaloneGoal(DefaultLifecycleExecutor.java:493)
        at org.apache.maven.lifecycle.DefaultLifecycleExecutor.executeGoal(DefaultLifecycleExecutor.java:463)
        at org.apache.maven.lifecycle.DefaultLifecycleExecutor.executeGoalAndHandleFailures(DefaultLifecycleExecutor.java:311)
        at org.apache.maven.lifecycle.DefaultLifecycleExecutor.executeTaskSegments(DefaultLifecycleExecutor.java:278)
        at org.apache.maven.lifecycle.DefaultLifecycleExecutor.execute(DefaultLifecycleExecutor.java:143)
        at org.apache.maven.DefaultMaven.doExecute(DefaultMaven.java:334)
        at org.apache.maven.DefaultMaven.execute(DefaultMaven.java:125)
        at org.apache.maven.cli.MavenCli.main(MavenCli.java:280)
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
        at java.lang.reflect.Method.invoke(Method.java:585)
        at org.codehaus.classworlds.Launcher.launchEnhanced(Launcher.java:315)
        at org.codehaus.classworlds.Launcher.launch(Launcher.java:255)
        at org.codehaus.classworlds.Launcher.mainWithExitCode(Launcher.java:430)
        at org.codehaus.classworlds.Launcher.main(Launcher.java:375)
[INFO] ------------------------------------------------------------------------
[ERROR] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] File 'web/pom.xml' does not exist
[INFO] ------------------------------------------------------------------------
[INFO] For more information, run Maven with the -e switch
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 1 minute 35 seconds
[INFO] Finished at: Thu Sep 20 20:22:49 CEST 2007
[INFO] Final Memory: 7M/22M
[INFO] ------------------------------------------------------------------------
 
It looks, therefore as though the AMP plugin hardcodes the 'web' module name - and expects only that module to exist, as opposed to allowing for the name to be picked up from the list of modules within the <module> tag in the base pom.xml.