You should be able to upgrade right to the latest versions of JIRA and JIRA Agile without any issues. Here's some documentation on upgrading JIRA. This lists all the possible ways of upgrading JIRA Agile. One thing to note is that the way JIRA Agile handles data is differently. As of JIRA Agile 6.4 we introduce lexoranking. When upgrading the reindex process will take unusually longer as it needs to build the lexorank tables. It should only take longer the first time around.
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