when you defined your own module, did you include all "provided" dependencies in module.xml so all dependencies of your module resources are included.
app server automatically adds some dependencies to your application based on what technologies you use (if you use jpa it will add javax.persistence module).
Thanks Tomaz, It was a great help.
I added following dependencies so far to my own module.xml and many ClassNotFoundExceptions are resolved:
<module name="javax.api" export="true"/>
<module name="org.apache.xalan" export="true"/>
I should now look for other dependencies that are missing.