Where is the configuration file?
The configuration file is definitely in $HOME/.bitcoin/. If you cannot see it, the most likely explanation is that you have not created it. Just use your favorite text editor to do so. As far as I can tell, bitcoind -daemon will run without bitcoin.conf being present and you will still get the message 'Using config file /home/user/.bitcoin/bitcoin.conf' in debug.log even when no file exists.