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Remy is correct when he says that debugging can be a real PITA when you are using a manifest file. A technique I’ve found useful is to monitor your web server logs while running your app to see exactly what resources your browser is requesting.
1) ssh into your server
2) cd to your log directory (prolly /var/log/httpd/ or /var/log/apache2/)
3) Run: sudo tail -f access_log
4) Reload your app in the browser; your request(s) should pop into the terminal.
When you are done watching the log, press Control-C to quit the tail process.
You can also inspect the ApplicationCache sqlite database manually using sqlite3 at the command prompt (with Safari on Mac, at least – not sure about others).
More here if y’all are interested: