If you want to modify the template file, you need a few more step to see the result of the modification on your browser.
First you have to generate a javascript file "App.template.
js" from the template file "App.template".
Then put this file and some other
js files together to Startup1_2_all.
js so that Web browser can download the modifiled
js file.
For more detail, you should check out ZimbraWebClient project from source code repository and see the build.xml file in it.
It is pretty long way so I still recommend css modification.