allow to specify arbitrary names for merged regions

@orlando I tested this with the input file you sent me. Please give it a try and let me know if anything is unclear. Otherwise please feel free to merge (doesn't conflict with anything else). Gracias.

Details: This fixes #36 (closed)

The configuration is now written to a text file that is evaluated at runtime. A template configuration is provided if you run without any argument. If one doesn't know all available regions, these can also be printed. See instructions at the top of the file. The logic is now more clear by defining a MergeConfiguration class.