Code cleanup

[riesentoaster]

Closes #35

• [x] Improve JavaDoc
• [x] Improve file/package structure
• [ ] More testing

[riesentoaster]

What's up with these commented lines in TraceFileToYamlConverter?

    /**
     * Convert the information in the @param traceFile to yaml code.
     * 
     * @param   traceFile to write to disk
     * @return  traceFile as yaml code
     */
    public static String toYaml(MorionInitTraceFile traceFile) {
        Map<String, Object> traceFileDump = new HashMap<>();
        traceFileDump.put(HOOKS, getHooksMap(traceFile));
        traceFileDump.put(STATES, getStatesMap(traceFile));
        // traceFileDump.put(INFO, traceFile.getInfo());
        // traceFileDump.put(INSTRUCTIONS, traceFile.getInstructions());
        return new Yaml().dump(traceFileDump);
    }

[floomm]

What's up with these commented lines in TraceFileToYamlConverter?

  /**
   * Convert the information in the @param traceFile to yaml code.
   * 
   * @param   traceFile to write to disk
   * @return  traceFile as yaml code
   */
  public static String toYaml(MorionInitTraceFile traceFile) {
      Map<String, Object> traceFileDump = new HashMap<>();
      traceFileDump.put(HOOKS, getHooksMap(traceFile));
      traceFileDump.put(STATES, getStatesMap(traceFile));
      // traceFileDump.put(INFO, traceFile.getInfo());
      // traceFileDump.put(INSTRUCTIONS, traceFile.getInstructions());
      return new Yaml().dump(traceFileDump);
  }

These are from the very beginning when I read and saved all trace file fields in every case. I remember, at the time you changed the data structure to only include hooks and states these were commented out. Because we thought we might need them again for the display part. But now having the MorionInitTraceFile and MorionTraceFile classes, we don't need them anymore.

So, they can be removed.