Your extract use 2.0.2 which is obviously wrong for what you are reporting. There are also chances that the type of resources your are filtering are linked to the issue.

I guess you want the issue resolved. If it's the case, provide a sample project to reproduce your issue, that's the strict minimum.

I was a bit under rush, so I just wanted to warn about this issue, I will prepare a more descriptive text and a sample project.
I use 2.0.2 as the filtering of webressouces is not working anymore with alpha version.

The file param.jsp contains properties which are set in the pom.xml.
when you run mvn clean package, these properties are replaced by the one defined in the corresponding profile.

Exemple :

mvn clean package -Dprofile1=1

param.jsp :

<c:set var="app_version" value="1.0-SNAPSHOT"/>
<c:set var="app_mainStyleSheet" value="profile1.css"/>

mvn clean package -Dprofile2=1

param.jsp :

<c:set var="app_version" value="1.0-SNAPSHOT"/>
<c:set var="app_mainStyleSheet" value="profile2.css"/>

This was working well with war plugin version 2.0.2 and not with the alpha version.

If the target file alredy exists, it is not overwriten (first win strategy).

However, we should copy the resources first (so that we can apply filtering). Unfortunately there is this stupid "do not copy if it is the webapp source" flag used for the war:inplace goal (this sounds very hackish to me btw)

Thanks for taking care of this ; it would be good if we could chat a bit to see how we're gonna solve this.

WarProjectPackagingTask#performPackaging
        ...
        metainfDir.mkdirs();
        handleWebResources( context );        
        handeWebAppSourceDirectory( context );
        handleDeploymentDescriptors( context, webinfDir, metainfDir );
        ....

The easy fix is to change handeWebAppSourceDirectory before handleWebResources.
IMHO it makes senses.
WDYT ?

handleWebAppSourceDirectory won't filter anything. This is the default goal used to copy the content of src/main/webapp.

<webResources>
<resource>
<filtering>true</filtering>
<directory>src/main/webapp</directory>
<targetPath></targetPath>
<includes>
<include>param.jsp</include>
</includes>
</resource>
</webResources>

Note the empty <targetPath></targetPath> instead of <targetPath>.</targetPath>