remove space in path
remove platform dependent check

the .input file may contain forward slashes / in the windows case,
that's not a problem.
presence of user-defined paths is checked.

this is done before anything else is executed.
If one of the given paths is not present, System.exit() is thrown.
leave flags in CKSolnList almost completely untouched.

instead of only printing the species info, just print everything chemkin
knows.

this causes bigger .ckcsv files, but at least all the stuff is in there.

This will definitely break the optimization code.
GetSolution prints mole fractions, and sens info

but still no rop info.

ROP is the biggest chunk of the .csv file.
temporarily comment out model value  setting

caused crashes.

will certainly break optimization code.
create a separate CKSolnList for each simulation

Earlier, CKSolnList was only created in the first simulation, copied
to the working dir, and then copied back to each of the other temp dirs.

Now, since each simulation can have a different CKSolnList because of
sensitivity flags for one particular species that was carried out in only
one simulation, this recipe was ready for disaster.

We now create a CKSolnList in each simulation by decorating the
chemkinRoutine in the RegularSimulationDecorator with a
CreateSolnListDecorator.

The method that modifies the CKSolnList is also moved that class.
The FirstSimulationDecorator is removed since redundant.

CKPackager makes no exception for the first simulation any more and
should therefore be faster.
allow BATCH keyword to run batch reactor simulations

batch reactor simulations are now allowed with reactor input files.

-the reactor input type in xml can now be BATCH

it will call the CKReactorGenericClosed routine of chemkin.

new keywords are defined for ReactorInput, ReactorSetupInput

the CKEmulationFactory is extended by returning the BatchDecorator
in case the BATCH keyword is passed in.

a small bug in BatchDecorator is fixed
add mass fraction parameter to ParameterEstimationDriver

a static flag flagUseMassFractions in ParameterEstimationDriver was
added and set as a command line argument to the Driver class

if the flag equals "--mass" then mass fractions will be printed instead
of the default mole fractions.

the GetSolutionDecorator is adapted to reflect this change.
CKPackager now stores model values

this ensures that parity plot mode works again
cut off mass or mole fractions from species names

by searching for "fraction" and subsequently cutting of the first 14
characters, both mole and mass fractions are correctly parsed.
Resolved bug: reinitialize total mole fractiona and mass fraction
use dependencies that are in lib folder (instead of home dir)
refactor parity writer in a way it sucks a little bit less

use commons-io to write to file
Merge branch 'master' of github.ugent.be:LCT/NBMT
add ant build file
untrack eclipse files, .gitignore

no need for them to share
create applications package and put main app in there
remove working dir from input xml file

we just take the working directory from "user.dir"
add example of how to use nbmt