webMathematica projects are very similar to other Mathematica projects, except that they also add web resources.
Mathematica resources work in a webMathematica project just as they work in other projects. Typically, they have an application project layout. This is because it is convenient to arrange the code to load in the server as an application. If you want to rearrange your Mathematica source code, for example locating it more deeply in the project, you would have to make a setting of the Mathematica project resources.
Mathematica resources can be deployed to the server; this is described in the deploying section.
Web pages that you want to deploy to the project need to be located in the WebPages folder. Its contents are deployed to the root of the web application. This is described in more detail, along with examples, in the Deploying section.
The file HTMLTest/test.html is created to test the project. Whenever you deploy to the server this file is opened in a web browser. Typically, it contains a link to a file in the server, but you could edit it to insert something else. If the file HTMLTest/test.html cannot be found then a web browser is not opened when you deploy the project.