Emma build caused SecurityException

Problem:
Web application throws below exception:

java.lang.SecurityException: Invalid signature file digest for Manifest main attributes
at sun.security.util.SignatureFileVerifier.processImpl(SignatureFileVerifier.java:221)
at sun.security.util.SignatureFileVerifier.process(SignatureFileVerifier.java:176)
at java.util.jar.JarVerifier.processEntry(JarVerifier.java:277)
at java.util.jar.JarVerifier.update(JarVerifier.java:188)
at java.util.jar.JarFile.initializeVerifier(JarFile.java:321)
at java.util.jar.JarFile.getInputStream(JarFile.java:386)
at org.apache.catalina.loader.WebappClassLoader.findResourceInternal(WebappClassLoader.java:2018)
at org.apache.catalina.loader.WebappClassLoader.findClassInternal(WebappClassLoader.java:1786)
at org.apache.catalina.loader.WebappClassLoader.findClass(WebappClassLoader.java:890)
at org.apache.catalina.loader.WebappClassLoader.loadClass(WebappClassLoader.java:1354)
at org.apache.catalina.loader.WebappClassLoader.loadClass(WebappClassLoader.java:1233)
at java.lang.ClassLoader.loadClassInternal(ClassLoader.java:319)

Solution:
It was caused by emma build, not sure of the exact root cause, but using standard (non-emma) build will not have this issue.

Notes:

1. Usually the exception is complaining the signed archive is corrupted
2. Emma is a open source java code coverage tool http://emma.sourceforge.net/