the latest version of in5 has two problems with the manifest.appcache.
1. The manifest file under "assets" was created but in the "html header" of each created page the link attribute is missing (<link rel="manifest" href="/manifest.appcache">
2. In the manifest.appcache file the link to the html files are not relative - so when develop local this can´t work on the server.
You can download a demo file and the html output here:
indesign demo file: