lin_cld_microphys.F90 is an internal-to-GFDL atmospheric physics parameterization which can be found in the GFDL AM4 public release. It has been replaced for external use by driver/SHiELD/GFDL_cloud_microphys.F90 and all files in master reference this file/module.
The lin_cld_microphys_mod is on the master branch, but not on the dev/gfdl branch.
Is it the lin_cld_microphys.F90 from master that you guys are using when building branch dev/gfdl?