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all.sh restores **/Makefile from git in case the version in the worktree was from doing a cmake in-tree build. Instead of doing this unconditionally, do it only if the toplevel Makefile seems to have been automatically generated (by cmake or otherwise, e.g. by mbedtls-prepare-build). This way all.sh no longer silently wipes changes made to Makefile but not committed yet. Signed-off-by: Gilles Peskine <Gilles.Peskine@arm.com>