feature/add-extract-module-python-script

Continuation of !2654 (closed)

Closes #1021 (closed) Closes #1037 (closed)

TODO:

• fix issue with quotations in patches (TODO: test shell script case - see explanation below)
• after getting rid of the patches the getCurrentTimeStamp function is now obsolete. We could remove it.
• test several situations
• change code using snake_case to camelCase
• squash commits, at least those from !2654 (closed)
• make sure that paths are printed correctly without intermediate ../ or .
• Allow untracked files in module dependencies (-> create patches for them)
• Fix generated CMakeLists to contain only one subfolder level
• Fix the missing opts file if dumux is not copied
• Apply patch in a correct order: untracked->uncommitted->unpublished.