The Project -> Generate TCL File for Project option generates a TCL file. It seems to be a file that can create a new Quartus project from scratch and add all the source files into it automatically. Once I have this TCL file, how am I supposed to run it from command-line? I don't think a normal TCL shell can execute this script.
Yes, you can actually create a project from scratch using TCL API from Quartus. At a DOS or shell prompt, you can run a script that contains that tcl code as shown here after you generate a tcl project.
quartus_sh -t script.tcl -project top -revision first
For more details regarding the API, in shell, quartus_sh --qhelp and there would be list of API tcl package for your scripting.
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