Updated README-hacking.md's checklist for better usability

After the checklist was applied in the 5th Indo-French Astronomy School, we
found some cases in the checklist that were extra (and thus had to be
removed), or were needed (and thus were added).

Also the non-necessary steps for a first commit were moved to a
separate/new section in the checklist for the people to add after doing
their first commit.

Also, the software part of the paper was moved to an appendix.

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