Select your project in the Package Explorer panel and then choose Project > Properties from the Flash Builder menu bar.
Select Flex Build Path > Add Project and select "flexcapacitor" library project. If you don't see this go back to the previous step and add in the Flex Capacitor library.
Next add the html-template folder. Click on Source Path and click Add Folder. Browse to the "html-template" folder. For example, it may look like this, "${DOCUMENTS}/flexcapacitor/html-template".
Click OK
If everything blows up that probably means your project is a Flex 3 project. Click on the flexcapacitor library project in the Package Explorer panel and go into Properties. Change the Flex SDK to Flex 3.x (any 3.2, 3.3, 3.4, 3.5, etc).
In the project Flex Library Build Path > Classes tab uncheck Containers/Group.
Click OK
It should now recompile.
You'll notice too that the "html-template" folder shows a red X through it. Right click on it and select Replace with Latest from Repository.
Finally, in your project copy the file, "[source path] html-template/index-template.html" in the to your "html-template" directory. This will overwrite what you previously had. So if you made modifications then just copy over the differences. Make sure also that the "scripts" folder is copied to your bin debug folder.