make it more clear what folders/files are re-generated vs imported

[dczielinski]

it's currently not clear that it doesnt overwrite the fit folder or that it imports the king altman result if it exist

one option would be to add an optional "clear folder" section at the start that would wipe any existing files associated with the notebook

[martamatos]

addressed in commit 902c4c6

see GAPD_v0.99 for what changed.
code added/changed in "Initializing the notebook" section:

removeInputFiles = False;
removeOutputFiles = True;

{workingDir, pathData, runFitScriptPath, inputPath, outputPath, bigg2equilibrator} = initializeNotebook[pathMASSFittingPackage, mainFolder, removeInputFiles, removeOutputFiles];