Revert "[modules] Don't leak -M flags for dependency file generation into the module"

This was failing tests on a bunch of bots:

http://lab.llvm.org:8011/builders/clang-hexagon-elf/builds/29919/steps/check-all
http://lab.llvm.org:8011/builders/clang-x86_64-debian-fast/builds/29627/steps/check-all
http://lab.llvm.org:8080/green/job/clang-stage1-configure-RA_check/9959/
http://lab.llvm.org:8080/green/job/clang-stage2-configure-Rlto_check/5591/

This reverts r244412

llvm-svn: 244414