Hey Dan,
First, it's worth mentioning that Hadoop doesn't really enforce a file stucture outside of the hdfs:///user/ directory. Not sure Hue will help you in that case any more than a simple "hdfs dfs -ls /"
In any case, Hue uses Makefiles to build it's environment. You need to be in a folder containing a Makefile for the Make targets to be resolved. For Hue, "apps" is such a target.
You use "cd" to change directories in a terminal.
For example,
$ cd ~ # go to home directory
$ git clone --depth=1 https://github.com/cloudera/hue.git # checkout Hue source
$ cd hue # go to hue directory
$ make apps
Personally, unless you are planning on developing some code, I would recommend not building from the source, at least from the master branch. The tarball package available at the Download link should be runnable on its own. If you do use the git sources, and you want to target a particular release, you should checkout the corresponding release branch.