By this command, you'll be creating a new .keystore file in $user_profile path. So, probably it is asking for a new password.
However, please try to use the default JAVA password, which is changeit . Otherwise, you'll have to add the tag keystorePass = 'userpassword' in the server.xml file.
Fir further details, please use the previous documentation.
Er, we have no idea. Jira needs to know what the password you have set on your keystore. If you don't know it, then contact whoever set it up for you. If you don't have a keystore, or you don't know the password, you'll have to create a new one and use that.
Have a look at http://docs.oracle.com/javase/1.4.2/docs/tooldocs/windows/keytool.html and http://www.sslshopper.com/article-most-common-java-keytool-keystore-commands.html for a more human friendly set of hints
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