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That is indeed the risk you run when using a PortableApp. Nothing new here.
Note that if the executables are not discovered on the drive itself then the launcher will fallback on the system search path. I assume anyone storing program binaries on a flashdrive is aware that there is a level of risk.
However, it is necessary in order to be fully portable (the goal of the launcher is to give choice) that the user is permitted to choose where to store the program binaries.
The way I see it, there is only a net gain over storing it on a vfat drive.
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