Is the idea that a developer would run a hot wallet and your PHP library on the server?
Exactly. My library is meant to be doing all the JSON-RPC-releated stuff to communicate with bitcoind to make receiving payments in various cryptocurrencies as simple as possible. Example code:
$client = new Client();
$payment = $client->createPayment();
$payment->setCurrency('BTC');
$payment->setAmount(0.01);
$payment->save();
print($payment->address);
Then, to check if user has paid:
$client = new Client();
$payment = $client->loadPayment($payment_id);
print($payment->status);
Maybe there is some way to modify wallet.dat file? I have found out that it's a Berkeley DB file. However, I'm afraid my script won't be able to edit it without root access. Additionally, modifying it while bitcoind is running may cause some troubles. And it HAS to be on all the time to update the blockchain...