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All calibre-protable.exe does is set a few environment variables and run calibre.exe. If you want to pass extra command line arguments to calibre.exe, simply write your own batch file to replace calibre-portable.exe
See the heavily commented calibre-portable.bat in the resources subdirectory of the calibre source tree for an example.
I could probably have calibre-portable.exe pass command line args to calibre.exe, except that command line processing on windows is such a pain, that I am reluctant to spend the time on it.
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