What is the purpose of a .jks keystore?

Is the private key of a certificate supposed to be stored in a .jks keystone?

Yes, if you own the certificate and it is stored there.

If yes - where does this get entered in? Using the keytool, it doesn't require one for creating a jks file.

That's because you can also use it as a truststore, which only contains trusted certificates.

To get the private key in there you will need to first convert it and its certificate to a PKCS#12 file using openssl, as answered in numerous questions here such as this.

If no - what is the purpose of a jks file? Why would my application need it instead of just reading in a certificate directly?

Because your application also needs the private key of the certificate.

And why does the keytool require a password to create a jks if it just contains a public key?

A keystore has a password because it is a security-related entity.

The purpose of a key store is to protect the privacy and integrity of cryptographic keys using password-based algorithms. Privacy means that the keys are kept secret; they can only be used by someone who knows the password; this is useful for private keys and secret keys. Integrity means that alteration of the keys can be detected by someone who knows the password; this is useful for public keys and secret keys.

Whether you should include the private key or not depends on what you are trying to do. If you are creating a key store for your server so that it can authenticate itself to clients, for example, then it should contain the private key. If you created a self-signed certificate, and want to give clients a key store so that they can authenticate your service, then it should not contain the private key.

If you have a pre-existing key pair, and want to import it to a JKS format key store, the easiest way might be to use OpenSSL to create a PKCS #12 format key store, then use keytool to convert that to a JKS key store. Normally, keytool expects to do key pair generation itself, and so the private key will be stored there from the beginning.

You should verify the integrity of a public key or a certificate before you use it to encrypt a message or verify a signature. Otherwise, an attacker can replace the key with one he owns and act as a man in the middle. If you simply read a public key from a file, you don't know it really belongs to your intended recipient. But if you store a password-based message authentication code with the public key, you can ensure that it hasn't been tampered with.