Fixed updateConfiguations call when pruning prep network

Discussed in #58. @jwallen made the change in 4ef7e32,
just missed this case.
Fix `getValue` call for input file writer

This fixes the website input file writer. There is
still more to add e.g. QM in the input file writer,
however this will prevent it from breaking (hopefully).
Merge pull request #210 from pierrelb/pDepPruning

Fixed updateConfiguations call when pruning prep network
Merge pull request #211 from pierrelb/webInpFileWriter

Fixes website input file writer