IOS – XCode: code signing entitlement file in command line

duti is a shell utility that enables using a text file to configure the default applications for file types and URL schemes.

For example save a file like this as ~/.duti:

com.gnu.Emacs public.plain-text all 
com.gnu.Emacs public.unix-executable all
org.videolan.vlc .mkv all

Then run duti ~/.duti.

You can install duti with brew install duti or by running wget https://github.com/fitterhappier/duti/archive/duti-1.5.2.tar.gz;tar -xf duti-1.5.2.tar.gz;cd duti-duti-1.5.2;./configure;make;sudo make install.

You can install OpenSSH in Cydia and use a SSH client (say, Panic's Prompt - look for it in the App Store), that makes a pretty nice terminal emulator for iOS.

As to running programs from the command line, sure, no problem, but none of them are designed to work in CLI. They don't retrieve/parse arguments, don't output...etc If you can get some out of Cydia or compile them yourself, it'll work, but I don't think you'll be able to command Apple's own apps that way.