There is no file with gitmodules or Externals_CLM.cfg in the fate directory.This indicates that you are using manage_externals but fates is using git-fleximod, try removing the
.gitmodules file from the fates directory and see if that solves the problem
or you can go to the CTSM/src/fates directory and manually checkout the fates code indicated by the
top level Externals_CLM.cfg file.
How can I remove them?