I have run into this same error. WIndows Xp and 2003, Java 1.5.0_12 and 1.6.0_01, Maven 2.0.6 and 2.0.7, IDEA 6.0.5.

The project I'm running against can be found at:

https://logan.carbonfive.com/svn/public/webapp-reference/tags/maven-idea-bug/

If there's anything I can to to help diagnose, let me know. If it's any help, I only started seeing this behavior very recently... I think it might have been introduced in the last week or two.

Ben, what version of IDEA are you using?

I'm using 6.0.5, but does that have anything to do with the ipr file generation?

I agree, I don't think it could. I manually fix my .ipr before even starting IDEA, so there's no chance that the IDE is mucking things up. It's a maven-plugin problem. Is there anything else we can could to help diagnose?

I am using maven 2.0.5 and do not encounter this issue. My colleague uses 2.0.7 (on the same project) and encounters this issue.

My idea project contains:
<module filepath="$PROJECT_DIR$/hermes.iml"/>
<module filepath="$PROJECT_DIR$/repository/repository.iml"/>
...

his contains:
<module filepath="$PROJECT_DIR$/c:/work/hermes.iml"/>
<module filepath="$PROJECT_DIR$/c:/work/repository/repository.iml"/>
...

Thanks to Christian I had something to test on. So I gave it a try. The top level .ipr file looks like this for me:

<component name="ProjectModuleManager"> 
    <modules> 
      <!-- module filepath="$$PROJECT_DIR$$/${pom.artifactId}.iml"/ -->  
      <module filepath="$PROJECT_DIR$/webapp-reference.iml"/>
      <module filepath="$PROJECT_DIR$/webapp-reference-core/webapp-reference-core.iml"/>
      <module filepath="$PROJECT_DIR$/webapp-reference-web/webapp-reference-web.iml"/>
    </modules> 
  </component>

This test was done using Maven 2.0.7 with Sun Java 1.5.0_11 on Windows XP.

So to me everything is working as expected.

This is what I get on my machine:

<component name="ProjectModuleManager"> 
    <modules> 
      <!-- module filepath="$$PROJECT_DIR$$/${pom.artifactId}.iml"/ -->  
      <module filepath="$PROJECT_DIR$/webapp-reference.iml"/>
      <module filepath="$PROJECT_DIR$/D:/Development/Projects/WAP-MVN/webapp-reference-core/webapp-reference-core.iml"/>
      <module filepath="$PROJECT_DIR$/D:/Development/Projects/WAP-MVN/webapp-reference-web/webapp-reference-web.iml"/>
    </modules> 
  </component>

$ mvn -v
Maven version: 2.0.7
Java version: 1.6.0_02
OS name: "windows xp" version: "5.1" arch: "x86"

I am also running this under cygwin, which might have something to do with it.

Same thing, but from a non-cygwin shell:

<component name="ProjectModuleManager"> 
    <modules> 
      <!-- module filepath="$$PROJECT_DIR$$/${pom.artifactId}.iml"/ -->  
      <module filepath="$PROJECT_DIR$/webapp-reference.iml"/>
      <module filepath="$PROJECT_DIR$/webapp-reference-core/webapp-reference-core.iml"/>
      <module filepath="$PROJECT_DIR$/webapp-reference-web/webapp-reference-web.iml"/>
    </modules> 
  </component>

Looks like cygwin IS the problem.

Great new Christian, now we're getting close.

I have a hunch that this is a case problem. To verify this I have added some debugging code and deployed a new 2.2-SNAPSHOT of this plugin. Would you mind trying it on your project using "mvn -X idea:idea". Post the results of the "[DEBUG] toRelative..." lines at the end of the build here.

Here's all of the toRelative output under cygwin.

Thanks Christian.

I you look at lines 7-8 in your file, you can see that the difference in case makes toRelative() produce the wrong results for the sub-project .iml files. Compare "d:\Development..." to "D:\Development...".

Now I just need to figure out a good way to solve this.

OK, new SNAPSHOT deployed with a possible solution.
Please give it a try and post your "toRelative..." output once again.

This is with the latest snapshot.

Fixed in SVN r556436.

Works for me. Thanks Dennis!

And for me. Thanks!