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pep8 specifies 4 space indentation. The use of 2 spaces is, I believe
a historical anomaly where certain large organizations such as google
chose 2 over 4 and have yet to make the switch.
Since there isn't too much code in binaryen today it seems reasonable to
make the switch.
Remove executable bit and #! from scripts that don't have
entry point.
Add missing licence test.
Move arg parsing into a function.
Remove legacy --only_prepare (with underscrore) argument.
