When rerunning CMake using the Ninja generator (specifically, when CMake is in the generating phase), it *deletes* all the generated Fortran module files. This forces the subsequent `ninja` invocation to rerun the Fortran compiler on the preprocessed versions, which regenerates the object files, which causes all downstream libraries to be relinked. This does *not* happen in the Makefile generator, where module files persist between CMake calls. [Example project](https://gitlab.kitware.com/sethrj/fortran-module-test) Locking one of the module files shows where the removal command actually happens: ``` -- Generating done CMake Error: Running '/usr/local/bin/ninja' '-C' '/Users/s3j/cmake-fortran-module/build-ninja' '-t' 'cleandead' failed with: ninja: error: remove(module/bar.mod): Operation not permitted CMake Generate step failed. Build files cannot be regenerated correctly. ``` This is using CMake 3.18.4 (and I replicated with the cmake master); and Ninja 1.10.1 (and I replicated with the `features-for-fortran` kitware branch as well).