We are working on an addition to the CFAST suite that will allow users to do this, but it's not ready yet. We've used Python to create the files and then run them with a Windows batch file. The CFAST repo contains a utility program
that creates a Linux and Windows script to run multiple CFAST runs. In Windows, it depends on CFAST and another utility, background.exe (that's installed as part of the FDS software but not yet CFAST), being in the Windows Path. The linux version is a bit more involved, but doable.
Alternatively, you can just create your own batch file by creating a list of the CFAST inputs files (for example, with a command like dir/b *.in > runall.bat, and editing the file to add the appropriate cfast.exe to the command line with a text editor (for example, Notepad will work, but Word creates its own format that's not directly callable from the command line). You can then run that file from the command prompt as simplly runall.bat (or whatever name you call it).