To anyone who would like to aggregate Cobertura's reports in a multi-module Maven project which has a large number of submodules and/or very long pathnames for each, then use James's patch given above but add a few lines of code into CoberturaReportMojo.java. If it is failing because of these long pathnames, the only thing you will notice is that your reports will say all complexities are 0 when they are not in fact 0.
What's happening is that it uses cmd.exe to run its commands, and then tries to include way too many, huge source files, which goes over the cmd.exe 8191 character limit, failing the report aggregation with a general exception.
Here's what you add to CoberturaReportMojo.java to fix it:
In private void executeReport(File curDataFile, File curOutputDirectory, List curCompileSourceRoots), add:
cmdLineArgs = new CommandLineArguments();
after you set the task defaults and specifics, but before you check the formatting. This is enough to change to using the command file to list all of the sources which need to be included instead of listing each explicitly on the command line.
You also need to add an import statement at the top:
Rebuild and install the plugin, and this should fix these problems. Hope it helps!