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Currently, Confluence does not provide an easy way to change the favicon.ico that will persist after an upgrade. If you want this feature, vote for this request on Jira. Otherwise, a good solution may be implemented using Apache's mod_rewrite.
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Make sure to change /wiki/ if you decided to deviate from this tutorial.
Finally drop a favicon.ico into your virtual host's root directory. In this example, /home/www.krypton.com/www/
System Profile
Using htop, initial setup without any spaces created is 396MB. The process itself uses VIRT=913M and RES=338M.