Handling security when deploying Java application

Question

I have a Java app (deployed as a JAR file) that allows file sharing through SLLSockets. If all users use the same certificate, file transfers are not secure, since it violates the core concept of asymmetric encrypted communication. Therefore, I understand that each user needs to have its own certificate. This brings up my first question:

1. How can you generate a certificate programmatically, and where would you store it ? I don't want users to have to generate their own certificate with keytool, then have to tell the app where it is located.

Now, let's say my first question is answered and each user has its own certificate. Prior to opening the SSL connection between two hosts, you need to add each other's certificate to the trustStore. The only way I know to achieve this is by exchanging them through Sockets (note that I am using JGroups to exchange Socket connection info). This brings up my next two questions:

2. How do you guarantee authentication and integrity when exchanging the certificates ?
3. How do you programmatically add the received certificate to the trustStore ?

Finally, this whole post brings up my fourth question:

4. Are the steps described above the correct way to send data securely between two hosts, using SSLSocket asymmetric encrypted communication ?

Answer 1

You don't need client certificates necessarily.

Could you not use username/password authentication?

You can still secure the transfer just by using a server certificate.

Client certs are also kind of a pain, and not entirely secure. They tie you to a machine, and evil processes can read them. Smart cards mitigate this, but aren't free.