java.lang.ClassNotFoundException / java.lang.NoClassDefFoundError after updating to EAP 6.4 CP9

Issue

• Getting the following error after applying Cumulative Patch (CP) 9 to EAP 6.4

Caused by: java.lang.NoClassDefFoundError: javax/ws/rs/core/UriInfo
        at java.lang.Class.getDeclaredFields0(Native Method) [rt.jar:1.7.0_95]
        at java.lang.Class.privateGetDeclaredFields(Class.java:2509) [rt.jar:1.7.0_95]
        at java.lang.Class.getDeclaredFields(Class.java:1819) [rt.jar:1.7.0_95]
        at org.jboss.as.server.deployment.reflect.ClassReflectionIndex.<init>(ClassReflectionIndex.java:57) [jboss-as-server-7.5.9.Final-redhat-2.jar:7.5.9.Final-redhat-2]
        at org.jboss.as.server.deployment.reflect.DeploymentReflectionIndex.getClassIndex(DeploymentReflectionIndex.java:68) [jboss-as-server-7.5.9.Final-redhat-2.jar:7.5.9.Final-redhat-2]
        ... 10 more
Caused by: java.lang.ClassNotFoundException: javax.ws.rs.core.UriInfo from [Module "custom-service.war:main" from Service Module Loader]
        at org.jboss.modules.ModuleClassLoader.findClass(ModuleClassLoader.java:213) [jboss-modules.jar:1.3.7.Final-redhat-1]
        at org.jboss.modules.ConcurrentClassLoader.performLoadClassUnchecked(ConcurrentClassLoader.java:459) [jboss-modules.jar:1.3.7.Final-redhat-1]

• Updating from 6.4.8 to 6.4.9 causes java.lang.NoClassDefFoundError

Caused by: java.lang.NoClassDefFoundError: javax/servlet/jsp/tagext/TagSupport
    at java.lang.ClassLoader.defineClass1(Native Method) [rt.jar:1.7.0_79]
    at java.lang.ClassLoader.defineClass(ClassLoader.java:800) [rt.jar:1.7.0_79]
    at org.jboss.modules.ModuleClassLoader.doDefineOrLoadClass(ModuleClassLoader.java:361) [jboss-modules.jar:1.3.7.Final-redhat-1]
    at org.jboss.modules.ModuleClassLoader.defineClass(ModuleClassLoader.java:482) [jboss-modules.jar:1.3.7.Final-redhat-1]
    ... 19 more
Caused by: java.lang.ClassNotFoundException: javax.servlet.jsp.tagext.TagSupport from [Module "deployment.test.ear:main" from Service Module Loader]
    at org.jboss.modules.ModuleClassLoader.findClass(ModuleClassLoader.java:213) [jboss-modules.jar:1.3.7.Final-redhat-1]
    at org.jboss.modules.ConcurrentClassLoader.performLoadClassUnchecked(ConcurrentClassLoader.java:459) [jboss-modules.jar:1.3.7.Final-redhat-1]
    at org.jboss.modules.ConcurrentClassLoader.performLoadClassChecked(ConcurrentClassLoader.java:408) [jboss-modules.jar:1.3.7.Final-redhat-1]
    at org.jboss.modules.ConcurrentClassLoader.performLoadClass(ConcurrentClassLoader.java:389) [jboss-modules.jar:1.3.7.Final-redhat-1]
    at org.jboss.modules.ConcurrentClassLoader.loadClass(ConcurrentClassLoader.java:134) [jboss-modules.jar:1.3.7.Final-redhat-1]
    ... 23 more

• We noticed when testing 6.4.9 that we suddenly had to add a number of dependencies in our ear's manifest.mf that we never had to add before. Specifically, they are javax.jms.api, javax.persistence.api, and javax.xml.ws.api.
  In all previous versions, including 6.4.8, we never had to add any custom dependencies in the manifest file. I didn't see any specific changes that would have caused this in terms of config file changes between 6.4.8 and 6.4.9 so I am wondering if this change was intended or if it is a bug.