When you have finished your application and want to use it in Mathematica, perhaps distributing it to it to other people, you can deploy your application. This can be done either to an archive, useful for distributing, or to a folder, which is useful if you want to use directly in Mathematica.
You can deploy your application to an archive with the export wizard. Open the export wizard from the application tools or from the menu bar by selecting File > Export > Mathematica and then choosing Application Archive. An example is shown below.
The wizard will add panes for different additions to the project that need to be treated specially for export. For example, if you have a J/Link project then you will see a page related to the Java classes. If you have documentation then the wizard will show you the documentation in the build it has found. An example follows.
If the documentation build did not exist or was not up to date, you would get a message at this point, asking if you would like to run the build.
You can deploy your application to a folder with the export wizard. This is very similar to deploying to an archive. Open the export wizard from the application tools or from the menu bar by selecting File > Export > Mathematica and then choosing Application Folder. An example is shown below.
In the wizard you have a chance to deploy directly into $UserBaseDirectory and $BaseDirectory. This is convenient if you want to start working with your application immediately. As explained in the section on Mathematica applications, these locations are provided by Mathematica so that you can install applications.