How could I dare posting here, being a beginner myself?
I learned a lot reading all these answers and there is only one thing I can throw in the discussion:
You can manage all this gathering of ideas and buildung of structures by the instrument of Literate Programming.
It helps me even for small scripts and I guess it will do a great job on large projects ... and it's easy to learn - I know what I say ;^)
Just my two cent ...
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