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Fix MCL long runtime

Workum, Dirk-Jan van requested to merge fix_long_mcl_runtime into develop

It was discovered by Zhitian Wu that pantools group increases the inflation of MCL up in a for-loop when it doesn't finish in time without notifying the user either. This hanging of MCL seems to be caused by it writing a lot of output that is not captured by Java. Therefore, implementing the following:

  • Remove the for-loop that increases the inflation parameter
  • Reduce the output of MCL by adding -V all.
  • Capture both STDOUT and STDERR of MCL properly.

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