Refactor configuration handling about modbat HOT 2 CLOSED

The problem is that some configuration entries (from Main.config) are copied by classes that use it. Some classes even have comments "copy of config" or similar.
These copies are convenient but there are too many of them, so the copied fields should be eliminated, and the corresponding field of Main.config should be used instead.
This task can be done step by step.

from modbat.

There are at least 7 cases of this happening:

1. In Dotify and Modbat:

./src/main/scala/modbat/mbt/Dotify.scala:    val fullOutFile = Main.config.dotDir + File.separatorChar + outFile
./src/main/scala/modbat/mbt/Modbat.scala:      val limit = Main.config.loopLimit

2. Copies from Main to other classes (in Main.scala):

    MBT.enableStackTrace = config.printStackTrace
    MBT.maybeProbability = config.maybeProbability
    MBT.runBefore = config.setup
    MBT.runAfter = config.cleanup
    MBT.precondAsFailure = config.precondAsFailure

from modbat.