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I want to protect several applications concurrently via the command line, because I'm creating a specific protected application for each customer. Is it possible?
Yes, you can do it with the specific command line that you use for Themida. In latest versions we have removed all intermediate files during protection, so there are no collisions when invoking Themida concurrently. Example:
Themida.exe /protect MyProject1.tmd
Themida.exe /protect MyProject2.tmd