I'm not smart enough to set up a development environment for maven plugins, but I believe the following changes to CoverageReport.java will do the trick:

In coverage.xml, you see

<coverage src="...
<class name="org.mydomain.MyClass$InnerClass0">
<file name="org/mydomain/MyClass.java">
<line ...
</class>
<class name="org.mydomain.MyClass$InnerClass1">
<file name="org/mydomain/MyClass.java">
<line ...
</class>
<class name="org.mydomain.MyClass">
<file name="org/mydomain/MyClass.java">
<line ...
</class>

But all three html reports are written to a file org/mydomain/MyClass.html.

At line numbers 283, 334, 357, and 367-375 in CoverageReport.java a file name based on Clazz.getName() instead of Clazz.getFile() should be created, e.g.

org/mydomain/MyClass$InnerClass0.html
org/mydomain/MyClass$InnerClass1.html
org/mydomain/MyClass.html

I'll leave the simple code fix to someone who knows how to build and deploy maven plugins.

PATCH to fix the problem described here which affects all inner classes.

The patch looks good, thank you Stephen.

Applied. Thanks.

This fix doesn't actually appear to have been applied to CVS.

I tried the patch and it works pretty well. However, the additional html files it generates don't seem to be linked from the allcallses-frame.html and package-frame.html files. I was able to fix that by using the getShortFileName() method on line 187 (CoverageReport.java) and remove the if-statement following it, so all classes get listed. I updated the patch, but I havent figured out how to put it in JIRA. (it's at http://forkalsrud.org/~erik/JCoveragePatch2.txt for now)

Also, setting up a developer environment for maven plugins turned out to be pretty simple. I did this using eclipse with these steps:

1 - File->Import... – "Checkout Projects from CVS"
2 - Select: "Create a new repository location"
3 - Enter values:
Host == cvs.apache.org
Repository Path == /home/cvspublic
User == anoncvs
Connection Type == pserver
4 - Select: User specified module name: "maven-plugins/jcoverage"
5 - Select: "Check out as project configured using the New Project Wizard"
6 - Select: "HEAD" and "Finish"
7 - Now, go though the regular eclipse project wizard.
I use MevenIde (http://mevenide.codehaus.org/) to add "Maven Nature" to
the project and cofigure all jars through the POM Synchronizer
8 - Go through steps 1-7, again, but this time, check out the module
"maven-plugins/plugin-parent"
(Also, you can "use an existing repoitory location" this time i.e. the
one you created in step 3)
9 - Right-click on CoverageReport.java and select: Team->Apply Patch...
to apply JCoveragePatch.txt
10 - Go to your eclipse workspace folder where the jcoverage plugin is,
and type "maven plugin:install" to try out your code changes.