Revert ".gitignore modified"

This reverts commit 5afed968d04b2052e96c30f5b94458a79d1d03ea.
Revert "Test model for DAEStepper"

This reverts commit 1b0c3813728d2c5d3c3f89fdaa39dfed490ddd8b.
Revert "Add kuzumoto_et_al_2007_SAN.em using ODEStepper"

This reverts commit 5ce1b5679216f9df62a2d842aef007cb1d292313.
Revert "Jedit X Coloring profiles for EM and C++"

This reverts commit a43d16260bcd6c687ed8a969d1bac849710561ca.
Revert "Atrium_model.em updated"

This reverts commit 0ab39e70988e67fd9517b770fef77544464a2de4.
Revert "himeno_et_al_2008_steadystate.em updated"

This reverts commit 3c46e55b6a65cd70a65dabef4f9bb8cc8556b6e6.
Revert "Adjust kuzumoto_et_al_2007_2.5Hz.Anoxya.em to the new Cytoplasm model"

This reverts commit 65c33d2fb42d9244cd7426c94651b1b6f821751c.
Revert "Modify IsotonicContractionAssignmentProcess.cpp"

This reverts commit 50cc5de5ba3a75325e8e44f1acf0c0c3b4d648d6.
Revert "Fix NaN occurence in Mitochondria"

This reverts commit 946179730c1e9fc5388e8b701f5c3598b2e8667a.
Revert "Discharge gsl_root_fsolve in IsotonicContraction"

This reverts commit a944062e3a57fc2bb10be2a2e68498c1fa24ccaa.