Add SpecFiltering package and put classes into that package. Remove dependency by extracting utility classes
Move MOPException and MOPNameSpace to Util as they are used in multiple modules and they don't depend/communicate with any other modules
Rename package name to be lower case
Put FileConverter to be inner class of JavaMOPOptions since it is only used there once
Move JavaMOPOptions to top-level since it is used only in JavaMOPMain and thus eliminating package commandline
Remove Utility class and put the method into Tool
Remove depedency from SystemAspect on JavaMOPMain by always excluding BaseAspect
Move AgentGenerator to agent
Move MOPProcessor to output since it is only used to generate code. Move MOPErrorChecker as well
Make a few classes in output to be package private
Pass option.verbose to AgentGenerator so it does not depend on MOPProcessor
Make some more classes in Parser to be private
Make some more classes in Parser to be private
Remove BaseAspect in SystemAspect
Merge pull request #124 from runtimeverification/refactor

Refactor