I have a directory like below:
/folder/b.js
/folder/jQuery.js
/folder/a.js
/folder/sub/c.js
I want to minify all these js files in one js file
I don't think you can do this with the uglify task alone, but you have a multitude of choices which might lead to your desired outcome.
A possible workflow would be first concatenating (grunt-contrib-concat) the files in order into one single file, and put this concatenated file through uglify. You can either define the order for concat in your Gruntfile, or you use on of those plugins:
First one would be https://github.com/yeoman/grunt-usemin, where you can specify the order in your HTML file, put some comments around your script block. The Google guys made it and it's pretty sweet to use.
Second one would be https://github.com/trek/grunt-neuter, where you can define some dependencies with require, but without the bulk of require.js. It requires changes in your JS code, so might not like it. I'd go with option one.