Reproducing the ISSUE:

1. create a new appfuse project
[kbucek@hpbook workspace]$ mvn archetype:create -DarchetypeGroupId=org.appfuse.archetypes -DarchetypeArtifactId=appfuse-basic-jsf -DarchetypeVersion=2.0 -DgroupId=org.foo -DartifactId=foo

2. run the full-source checkout
[kbucek@hpbook workspace]$ cd foo/
[kbucek@hpbook foo]$ mvn appfuse:full-source

OUTPUT:
[INFO] Scanning for projects...
[INFO] Searching repository for plugin with prefix: 'appfuse'.
[INFO] ----------------------------------------------------------------------------
[INFO] Building AppFuse JSF Application
[INFO] task-segment: [appfuse:full-source]
[INFO] ----------------------------------------------------------------------------
[WARNING] POM for 'org.hibernate:jtidy:pom:r8-20060801:runtime' is invalid. It will be ignored for artifact resolution. Reason: Parse error reading POM. Reason: TEXT must be immediately followed by END_TAG and not START_TAG (position: START_TAG seen ...<licenses>\n\t\t\t<license>... @12:13) for project org.hibernate:jtidy at /opt/dist/maven/repo/org/hibernate/jtidy/r8-20060801/jtidy-r8-20060801.pom
[INFO] [appfuse:full-source]
[INFO] [AppFuse] Installing source from data modules...
[INFO] [AppFuse] Installing source from service module...
[INFO] [AppFuse] Installing source from web-common module...
[INFO] [AppFuse] Installing source from jsf module...
[INFO] [AppFuse] Source successfully exported, modifying pom.xml...
[INFO] [AppFuse] Removing maven-warpath-plugin...
[INFO] ------------------------------------------------------------------------
[ERROR] FATAL ERROR
[INFO] ------------------------------------------------------------------------
[INFO] Couldn't rename temporary file /tmp/replace1728014005.txt
[INFO] ------------------------------------------------------------------------
[INFO] Trace
Couldn't rename temporary file /tmp/replace1728014005.txt
        at org.apache.tools.ant.taskdefs.optional.ReplaceRegExp.doReplace(ReplaceRegExp.java:431)
        at org.apache.tools.ant.taskdefs.optional.ReplaceRegExp.execute(ReplaceRegExp.java:491)
        at org.appfuse.mojo.installer.InstallSourceMojo.removeWarpathPlugin(InstallSourceMojo.java:609)
        at org.appfuse.mojo.installer.InstallSourceMojo.execute(InstallSourceMojo.java:207)
        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:597)
        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] ------------------------------------------------------------------------
[INFO] Total time: 46 seconds
[INFO] Finished at: Thu Sep 20 14:29:24 CEST 2007
[INFO] Final Memory: 8M/116M
[INFO] ------------------------------------------------------------------------

This issue is not really caused by AppFuse, as the trace indicates it comes from Ant 1.6.5 (as appfuse-maven-plugin uses this version of Ant).
The Ant bug could be found here: http://issues.apache.org/bugzilla/show_bug.cgi?id=34633

In my case changing the dependency from Ant 1.6.5 to 1.7.0 did solve this issue. Here is the relevant part of 'appfuse-maven-plugin-2.0.pom' from my local repository:

<!--
        <dependency>
            <groupId>ant</groupId>
            <artifactId>ant</artifactId>
            <version>1.6.5</version>
        </dependency>
        <dependency>
            <groupId>ant</groupId>
            <artifactId>ant-optional</artifactId>
            <version>1.5.3-1</version>
        </dependency>
-->
        <dependency>
            <groupId>org.apache.ant</groupId>
            <artifactId>ant</artifactId>
            <version>1.7.0</version>
        </dependency>
        <dependency>
            <groupId>org.apache.ant</groupId>
            <artifactId>ant-nodeps</artifactId>
            <version>1.7.0</version>
        </dependency>


Other users reproducing this bug from the forum: http://www.nabble.com/Error-with-appfuse%3Afull-source-tf4101432s2369.html#a11663469