The second part of your question, regarding filenames - Perl "does the right thing". So, just use Unix-style filenames and you'll be just fine.
With regards to commandline options ... the thing I did when I had a Perl app that ran on both was to have a batchfile in Windows that had the commandline options I wanted and had it launch the Perl app. It was just simpler that way, plus it stayed within the GUI nature of Windows, to just double-click on some batchfile on the desktop.
Just as a warning, if you have an application that is a commandline app that binds STDIN and STDOUT to be descriptors, this will not work under windows. You will have to set up a telnet server, then telnet to yourself to get this descriptor behavior. There is a way to check which OS you're on (I don't remember which), then bring in the right modules to do the right thing.
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