How can i have makefile/shell script call /Applications/application.app?
To use the Emacs.app from shell you need the unix executable embedded inside it. It is at Emacs.app/Contents/MacOS/Emacs (I don't have this version of emacs so the capitalisation might differ)

An alternative is to use open to start any app from the workspace using open.

e.g. 

open -a Emacs.app --args &lt;all those passed to emacs&gt;