1) The shortcuts are indeed yet another way to issue site commands, which makes your original suggestion indeed a little obsolete
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2) Allrighty, at first i couldn't see a way to implement this without scripting support but now i do think this can be done without much effort. You should have an option in the preferences called "transfer as" and put all replacing characters there. Especially "%20" (space) replaced bij a "." would come in handy for a lot of users i think, since much ftpd's don't accept spaces. I do know however that the options in preferences are really outgrowing the space available there so we should crosses our fingers that Bigstar finds a little place for this
.