I recently launched a JasperServer BI Proffesional for AWS. I am looking to custmoize the UI. Where is the root directory for JasperServer found? From what I have read, files found within are those needed to be edited to customize. It is a standard medium instance type if that makes a difference.
If you want to do UI customization you can do those by using JasperServer Themes. Which are CSS driven and stored in the JasperServer Repository. You will have to access the server as jasperadmin to access the Themes Folder. By right clicking on the default theme you can download the full css and images to customize that.
Remember that if you do not define a css file or image in your theme it will be inherited from the default theme. I've attached a sample theme for Jasper 5.x (GreenBay.zip)
More information about this in Chapter 5 of the JRS Admin Guide http://community.jaspersoft.com/documentation
Also check this article (the samples there are for JRS 4.5 but the same concept applies) http://community.jaspersoft.com/wiki/jaspersoft-themes