I just tried to run pslatex (which is a shell-script) with run.exe. And actually, it won't run. There is a box saying "Error: could not start c:\cygwin\bin\pslatex". Well, it's not an exe-file. It's basically a textfile to windows. Hence the error, i guess.
Now i wonder, if it's already safe or if it would be possible to use cygwin API (for example execve) from run.exe. To fix all the issues, run.exe really would have to use cygwin to start the command since only that will resolv all the issues (analysing the shebang, following symlinks, etc.). Just modifying the CreateProcess won't do. Or we would have to rewrite all the shebang/symlink stuff ourselves which is error prone.
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