The HTML5 Boilerplate build script can auto generate your manifest.appcache file but it doesn’t out of the box.
Slightly hidden away in the docs:
To enable the appcache, just uncomment the file.manifest line in the project.properties file. It’ll create a manifest.appcache file and wire it all up.
You’ll find the project.properties file in build/project.
Now just do ant build and your HTML5 manifest file will be created and automatically referenced in your HTML file.