Merge: src/Makefile: use peflags to bootstrap on windows

Inject automatically call to peflags on the 2 first steps of the bootstrap.

Other executables (those in bin/ and those compiled by the user) are not peflaged since it does not seems that useful in general.

Pull-Request: #1932
Reviewed-by: Alexis Laferrière <alexis.laf@xymus.net>