Many of the above aspetcs will save you a lot of time when you incrementally extend software over time from simpler to more complicated problems. In particular, you will benefit from many good habits:

1. New code is added in a modular fashion to a library (modules)
2. Programs are run through convenient user interfaces
3. It takes one quick command to let all your code undergo heavy testing
4. Tedious manual work with running programs is automated,
5. Your scientific investigations are reproducible, scientific reports with top quality typesetting are produced both for paper and electronic devices. Use version control software like git and repositories like github