(Note that when you're talking about "keystore" in your question, you're in fact talking about the trust store (which is a keystore). More details on this unfortunately confusing Java terminology are in this answer.)
My application will only make calls to a single server so if there was
a way to bypass the self-signed restrictions, and never consult
keystores, it wouldn't be a security problem, but is there a way to do
this?
Actually, it would be a security problem. Your application may indeed be intended to call only a single server, but the trust store is precisely there to help make sure you're connecting to the machine you intended to connect to. Without it, you wouldn't be able to know whether you're connecting to that server or a MITM server.
If you want the security provided by SSL/TLS, don't bypass these rules. (In particular, don't use a trust manager that will accept any certificate.)
I've looked around and the only solutions I've found is to add the
certificate to the java key store, but this is a problem for me
because I have no control over when or how they update java, and I've
read that the keystore isn't preserved between updates, and I have no
access to the system outside of the JVM.
Quoting myself from this answer (to a more specific question):
The right way is to import this self-signed certificate into the client's trust store, using keytool
for example:
keytool -import -file server-cert.pem -alias myserver -keystore mytruststore.jks
You can either do it directly in the JRE's trust store (lib/security/cacerts), which may lack some flexibility, or do it in your own copy of this file, which you then set as the trust store (the default password is changeit
or changeme
on OSX). You configure this truststore globally for your application using the usual javax.net.ssl.trustStore*
system properties (e.g. -Djavax.net.ssl.trustStore=mytruststore
system property (and -Djavax.net.ssl.trustStorePassword`). [...]
You don't actually have to use the trust store provided by the JRE (and which may be updated regularly). You could import your self-signed cert into a new empty keystore, which you'll use as a trust store within your application (don't import the private key with it). How to discuss trust store management was in fact discussed in this question: nothing prevents you from using a different trust store specifically for your application or part of it (and in fact Sun/Oracle make no guarantee as to the suitability of the default trust store).
I'm building an application that needs to open self-signed HTTPS SSL
URLs in java. I've learned that you can bypass the SSL problems by
adding a call to HttpsURLConnection.setDefaultHostnameVerifier() where
you say what hostnames are allowed.
While it may indeed by slightly less of a problem if you only have a single self-certificate in your trust store, host name verification is also an essential component of the security provided by SSL/TLS. Don't bypass it, verify that the certificate you're connecting to matches the name you're trying to connect to. (To make an analogy, if you want to check someone's identity, you not only want to check the their passport was emitted by a country whose passports you trust, but you'll also want to check they have the right name inside, otherwise you could be in front of anyone from that country.)
Making the CN=
RDN of the Subject Distinguished Name of your self-signed certificate be the host name of the server should be enough, although it's the legacy way of doing it. You may also want to add the Subject Alternative Name extension. More on this in this answer.
Generally speaking do not bypass the SSL "problems". These mechanisms are precisely in place to make the usage of SSL/TLS secure.