Config-file parsing order

In the case where the main config file contains an include option, the precedence for parsing options is important. I was under the impression that included files should have lower precedence than the file from which they are included. This way, certain options of the default config file (which should be version-controlled) can be overwritten by a local config file, which includes the default file. This is very handy for specifying sample locations on different clusters.

The current implementation gives precedence from tags in included config files. I suggest to change this behaviour.

Command-line options should always have precedence.