I've installed JIRA in a directory, .../confluence/jira-6.0.5/. This directory holds jira/ and jira-home/. Is there a way to move the jira/ and jira-home/ directories into the confluence/ directory?
I wouldn't do this. You should have separate directories for confluence and jira, otherwise you could end up with clashing names. By all means do something like .../atlassian/confluence and .../atlassian/jira, but do not just do .../confluence (and point both Jira and Confluence to use that as their home)
Once you've worked out a sensible tree structure, then Rambanam's link will tell you how to relocate everything safely
Yes, and that's easier, because it doesn't really care where they are. As long as you preserve the structure and file ownership/rights, you should be able to simply move the whole lot.
(Ooops, I forgot, "and don't put the application in the home directory")
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