Extraction: fix bugs 5177 and 5240 (and also indirectly bug 4720)

 Avoid Anomaly (or Assert False) when a module signature contains
 an applied functor followed by a "with Definition" or "with Module"

 Also fix the dependency computation in presence of a "with Definition"

 Concerning 4720, the code extracted out of this bug report was suboptimal
 in Coq 8.4 (it was compilable, but could have probably been tweaked into a
 real issue producing faulty code).
 But the example of 4720 (and some variants of it) was broken since 8.5,
 for the same reasons as 5177 and 5240. And the good news is that after
 these repairs, the example of bug 4720 is now extracted to correct code
 (the "with" is preserved).

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