Properly handle ordering of -w and -native-compiler

Warnings are handled as injection commands, interleaved with options
and requires. Native compiler impacts require, so we must convert
"yes" to "no" before handling injections. As such the semantic
handling of the native command line argument must be separated from
the emission of the warning message, which this PR implements.

Fix #13819

In principle the other 2 cwarning in coqargs
(deprecated spropcumul and inputstate) should be moved to injections
too, but since they're deprecated I can't be bothered.

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