I'm looking to write something that can enumerate and use (to sign) certificates in CurrentUser/My and LocalMachine/My, but I haven't been able to find anything for the Windows cert store, only Java's own secret store. This link looks promising, but I can only use what ships with Java.
I found this question asked on SO before, but it's from five years ago, which is a long time in computer years. Thanks!
Start Java with -Djavax.net.ssl.trustStoreType=WINDOWS-ROOT
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See https://www.oracle.com/technical-resources/articles/javase/security.html for more information.