adjust gitignore for changed folder structure

.gitignore

@@ -1,52 +1,51 @@
 # Ignore specific files and directories
-/LEMS/*.dat
+**/LEMS/*.dat
 SBML/*.dat
 x86_64
 i386
 umac
-/SBML/jsbml.log
+**/SBML/jsbml.log
 Brian/results/*.dat
-/NeuroML2/RS_v.dat
-/NeuroML2/LEMS_Test_nrn.py
-/NeuroML2/LavrentovichSBML.mod
-/NeuroML2/RS.mod
-/NeuroML2/RS_Iext.mod
-/NeuroML2/SBML.dat
-/NeuroML2/time.dat
-/NeuroML2/LEMS_Test2_nrn.py
-/NeuroML2/LavrentovichA.mod
-/NeuroML2/LavrentovichB.mod
-/NeuroML2/LavrentovichC.mod
-/Brian/Lavrentovich2008_Ca_Oscillations.dat
-/LEMS/BIOMD0000000184_LEMS_brian.py
-/LEMS/BIOMD0000000184_LEMS_brian2.py
-/NEURON/*.dat
+**/NeuroML2/RS_v.dat
+**/NeuroML2/LEMS_Test_nrn.py
+**/NeuroML2/LavrentovichSBML.mod
+**/NeuroML2/RS.mod
+**/NeuroML2/RS_Iext.mod
+**/NeuroML2/SBML.dat
+**/NeuroML2/time.dat
+**/NeuroML2/LEMS_Test2_nrn.py
+**/NeuroML2/LavrentovichA.mod
+**/NeuroML2/LavrentovichB.mod
+**/NeuroML2/LavrentovichC.mod
+**/Brian/Lavrentovich2008_Ca_Oscillations.dat
+**/LEMS/BIOMD0000000184_LEMS_brian.py
+**/LEMS/BIOMD0000000184_LEMS_brian2.py
+**/NEURON/*.dat
 *.gv*
-/LEMS/BIOMD0000000184_LEMS.png
-/NeuroML2/*.png
-/tests.log
-/NeuroML2/ex9.dat
-/LEMS/tmp
+**/LEMS/BIOMD0000000184_LEMS.png
+**/NeuroML2/*.png
+**/tests.log
+**/NeuroML2/ex9.dat
+**/LEMS/tmp
 arm64
-/NeuroML2/*.mod
-/NeuroML2/*_brian2.py
-/NeuroML2/*_nrn.py
-/NeuroML2/*.dat
-/NeuroML2/report.*.txt
-/SBML/*.pdf
-/SBML/ex9.csv
-/SBML/hr.csv
-/test_suite/semantic/
-/test_suite/semantic_tests_with_sedml_and_graphs.v*.zip*
+**/NeuroML2/*.mod
+**/NeuroML2/*_brian2.py
+**/NeuroML2/*_nrn.py
+**/NeuroML2/*.dat
+**/NeuroML2/report.*.txt
+**/SBML/*.pdf
+**/SBML/ex9.csv
+**/SBML/hr.csv
+**/test_suite/semantic/
+**/test_suite/semantic_tests_with_sedml_and_graphs.v*.zip*
 .vscode
-/BioModels/cache
-/BioModels/tmplocalfiles
+**/BioModels/cache
+**/BioModels/tmplocalfiles
 __pycache__
 venv
-/SBML/.DS_Store
-/SBML/LEMS_NML2_Ex9_FN_missing_xmlns.omex
-/SBML/output
-*.egg-info/
+**/SBML/.DS_Store
+**/SBML/LEMS_NML2_Ex9_FN_missing_xmlns.omex
+**/SBML/output
 
 # Byte-compiled / optimized / DLL files
 __pycache__/