commit-doc-tree: make docdirectory configurable
Fix NPE in result writing code

16:12:52.691 I o.t.s.n.g.ResultWriterHDF5 - Writing grid concentrations at time 0.9999999999999176
Exception in thread "main" java.lang.RuntimeException: java.lang.NullPointerException
        at org.textensor.stochdiff.numeric.grid.ResultWriterHDF5.writeGridConcs(ResultWriterHDF5.java:143)
        at org.textensor.stochdiff.numeric.grid.SteppedStochasticGridCalc.run(SteppedStochasticGridCalc.java:343)
        at org.textensor.stochdiff.SDCalc.run(SDCalc.java:54)
        at org.textensor.stochdiff.StochDiff.main(StochDiff.java:73)
Caused by: java.lang.NullPointerException
        at org.textensor.stochdiff.numeric.grid.ResultWriterHDF5._writeGridConcs(ResultWriterHDF5.java:155)
        at org.textensor.stochdiff.numeric.grid.ResultWriterHDF5.writeGridConcs(ResultWriterHDF5.java:141)
        ... 3 more
ResultWriterHDF5: fix writing of concentration data
util: add utility to combine jars

Useful for manual creation of hdf5 jars.
HDF5ResultWriter: write times and specie ids
Add python scriplet to visualize part. numbers
ResultWriterHDF5: write region labels too
Move trivial initialization code to helper func.
Stochastic: extract a function to randomly round
Stochastic: refactor negative ngo checking
Stochastic: extract some ngo calculations to a function
Stochastic: refactor intlogs a bit more
Extract array copying into a separate function
Remove some braces and add FIXMEs
Stochastic: remove two unused methods