Configuration file update

[changliao1025]

The configuration file will be updated after the pyflowline simulation.
changliao1025/pyflowline#31
However, should this be done by the main program or the sub-program is not decided.
The main configuration is passed to pyflowline, so there are essentially the same.
It is more straightforward to let pyflowline hand this because the basin config is within pyflowline.

[changliao1025]

An issue that arises when letting pyflowline export configurations is that the output workspace needs update.
So maybe letting the main program deal with it is easier.