First configure logging.properties to TRACE log org.jboss.modules.

1. Add org.jboss.modules to the logger names that need to be configured.
2. Set logger.org.jboss.modules.level to TRACE
3. Do not forget to comment out the threshold of the FileHandler (or ConsoleHandler)

Your logging.properties will then look like:

# Additional logger names to configure (root logger is always configured)
loggers=org.jboss.as.config,org.jboss.modules

# Dump system environment at boot by default
logger.org.jboss.as.config.level=DEBUG

logger.org.jboss.modules.level=TRACE

# Root logger level
logger.level=${jboss.boot.server.log.level:INFO}
# Root logger handlers
logger.handlers=FILE,CONSOLE

# Console handler configuration
handler.CONSOLE=org.jboss.logmanager.handlers.ConsoleHandler
handler.CONSOLE.properties=autoFlush
handler.CONSOLE.level=${jboss.boot.server.log.console.level:INFO}
handler.CONSOLE.autoFlush=true
handler.CONSOLE.formatter=PATTERN

# File handler configuration
handler.FILE=org.jboss.logmanager.handlers.FileHandler
#handler.FILE.level=DEBUG
handler.FILE.properties=autoFlush,fileName
handler.FILE.autoFlush=true
handler.FILE.fileName=${org.jboss.boot.log.file:boot.log}
handler.FILE.formatter=PATTERN

# Formatter pattern configuration
formatter.PATTERN=org.jboss.logmanager.formatters.PatternFormatter
formatter.PATTERN.properties=pattern
formatter.PATTERN.pattern=%d{HH:mm:ss,SSS} %-5p [%c] %s%E%n

Boot up either standalone or the domain and take a look at boot.log. There will be a stacktrace similar to:

13:10:53,891 TRACE [org.jboss.modules] Failed to define class org.jboss.as.ejb3.EJB3Extension in Module "org.jboss.as.ejb3:main" from local module loader @7d2452e8 (roots: /home/carlo/work/jboss-as/build/target/jboss-7.0.0.Alpha2/modules): java.lang.LinkageError: Failed to link org/jboss/as/ejb3/EJB3Extension (Module "org.jboss.as.ejb3:main" from local module loader @7d2452e8 (roots: /home/carlo/work/jboss-as/build/target/jboss-7.0.0.Alpha2/modules))
    at org.jboss.modules.ModuleClassLoader.defineClass(ModuleClassLoader.java:374) [:1.0.0.Beta13]
    at org.jboss.modules.ModuleClassLoader.loadClassLocal(ModuleClassLoader.java:250) [:1.0.0.Beta13]
    at org.jboss.modules.ModuleClassLoader$1.loadClassLocal(ModuleClassLoader.java:70) [:1.0.0.Beta13]
    at org.jboss.modules.Module.loadModuleClass(Module.java:486) [:1.0.0.Beta13]
    at org.jboss.modules.ModuleClassLoader.findClass(ModuleClassLoader.java:178) [:1.0.0.Beta13]
    at org.jboss.modules.ConcurrentClassLoader.performLoadClass(ConcurrentClassLoader.java:270) [:1.0.0.Beta13]
    at org.jboss.modules.ConcurrentClassLoader.access$400(ConcurrentClassLoader.java:42) [:1.0.0.Beta13]
    at org.jboss.modules.ConcurrentClassLoader$LoaderThread.run(ConcurrentClassLoader.java:339) [:1.0.0.Beta13]
Caused by: java.lang.NoClassDefFoundError: org/jboss/as/server/Extension
    at java.lang.ClassLoader.defineClass1(Native Method) [:1.6.0_22]
    at java.lang.ClassLoader.defineClassCond(ClassLoader.java:632) [:1.6.0_22]
    at java.lang.ClassLoader.defineClass(ClassLoader.java:616) [:1.6.0_22]
    at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:141) [:1.6.0_22]
    at org.jboss.modules.ModuleClassLoader.defineClass(ModuleClassLoader.java:370) [:1.0.0.Beta13]
    ... 7 more
Caused by: java.lang.ClassNotFoundException: org.jboss.as.server.Extension from [Module "org.jboss.as.ejb3:main" from local module loader @7d2452e8 (roots: /home/carlo/work/jboss-as/build/target/jboss-7.0.0.Alpha2/modules)]
    at org.jboss.modules.ModuleClassLoader.findClass(ModuleClassLoader.java:186) [:1.0.0.Beta13]
    at org.jboss.modules.ConcurrentClassLoader.performLoadClass(ConcurrentClassLoader.java:270) [:1.0.0.Beta13]
    at org.jboss.modules.ConcurrentClassLoader.loadClass(ConcurrentClassLoader.java:52) [:1.0.0.Beta13]
    ... 12 more

Clearly this shows that org.jboss.as.server is the missing dependency.

Why is this such a hassle?

For that we need to take a look in the JDK source ServiceLoader.java:

    public S next() {
        if (!hasNext()) {
             throw new NoSuchElementException();
        }
        String cn = nextName;
        nextName = null;
        try {
             S p = service.cast(Class.forName(cn, true, loader)
                   .newInstance());
             providers.put(cn, p);
             return p;
        } catch (ClassNotFoundException x) {
             fail(service,
                  "Provider " + cn + " not found");
        } catch (Throwable x) {
             fail(service,
                  "Provider " + cn + " could not be instantiated: " + x,
                  x);
        }
        throw new Error();        // This cannot happen
    }

If it encounters a ClassNotFoundException it doesn't emmit which class it can not find. Also the original exception is swallowed, so any diagnostic information within is lost.

They got one thing right though: fail. ;-)