Is it possible to specify functions in a MAP file from the command line? So I can dynamically change the functions to virtualize from my build system

Please, create a file with the same name as your MAP file but with the ".CRM" extension.

You can edit the CRM file and add lines with functions from your MAP file to be protected. If you want to protect a function called "MyFunction@8" and "FunctionA@12@13", you should write the following in your .CRM file:

|MyFunction@8|1|1

|FunctionA@12@13|1|1

Make sure that the name matches exactly the one in your MAP file. The values "|1|1" are just dummy values which will be recalculated by Code Virtualizer with the right file offsets where the function is located.