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At my company we already had a proper SSL certificate so I was able to skip a good third of the pdf that discusses in detail the proper way to generate the CSR and to create the certificate. WebHelpDesk recommends the use of a program called Portecle a java based utility that takes your certificates and creates a java keystore (.JKS). This is the file that actually secures Web Help Desk.
What I struggled with for a while as a System Administrator with little experience in the SSL realm was that no matter how many ways I tried to install the certificate for use on my server users would still get warnings saying that the certificate was not trusted. Through some trial and error and luck I figured out the proper steps to making sure that all of your services and your users can use SSL without the heartache of untrusted warning messages. The steps to follow are simple: