build: store dependencies as lists

In Python sets are unordered, so iterating them after converting to a list
always leads to different results. The code iterated on them to collect all
the flags to pass to the compiler, and since the order of the flags changed,
waf would rebuild all of the C files. Seems like in Python 2 this worked as
expected by pure chance.

This commit stores the sets as lists, and converts them to sets when the set
operations are needed.

Fixes #363

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