The customer had the initial problem reported as:

1. In admin I don't have the Plugin Repository menu option
2. Scan or upload of a plugin leads to a null pointer exception (see attached logfile)
3. On startup I see log messages like "The module 'macro' in plugin 'Attachments Macros' is in the list of excluded module descriptors, so not enabling." (I see a message like this for
every plugin.)

The customer fixed this problem locally by applying the following patch:

I've found what is causing the plugin problem in WebSphere 5.1.10.
In the class com.atlassian.confluence.util.ClasspathUtils there is a method getThreadContextClasspath().

In this method there is this statement: urls.addAll(Arrays.asList(((URLClassLoader)classLoader).getURLs()));
I debugged that getURLS() returns null thus causing a nullpointer.

At startup this nullpointer is swallowed. The only thing happening is that all plugins are rejected.
When later on you scan for plugins (in the mange plugins screen) than an error screen and a stacktrace is produced.

I've changed the code a bit:

URLClassLoader urlc = (URLClassLoader) classLoader;
URL[] urls2 = urlc.getURLs();
if (urls2 != null) { urls.addAll(Arrays.asList(urls2)); urlClassLoaderFound = true; }