Use the Ant Build Target
You will find the results in the ROOT\build\clientapi_docs folder. Click on the "index.html" file to see your new API reference site.
If you need to alter the output template, you can find the JsDoc Toolkit templates in the ROOT\tools\jsdoc-toolkit\templates folder.
Use an Alternative Build Method
You can also build the documents directly from within the jsdoc-toolkit folder.
First, place your annotated .js files in a folder called "clientapi" in the jsdoc-toolkit folder (<JSTOOLKIT> in the code snippet below). Then use a command line similar to the following to generate the docs:
C:\<JSTOOLKIT>>java -jar jsrun.jar app\run.js clientapi -t=templates\jsdoc
You will find the resulting API doc files a folder called "out" in your jsdocs-toolkit folder. Click on the "index.html" file inside the jsdocs folder inside "out" to see your new API reference site.