Differences between JAR vs. ZIP distribution?
What are the differences between the JAR and ZIP distributions of YouTrack 6? Are there advantages/disadvantages between the two distributions?
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JAR distribution allows you to run YouTrack as a stand-alone Java process. If you'd need to install this within any custom web server, JAR is your choice.
ZIP assumes installation.
Details can be found here http://confluence.jetbrains.com/display/YTD6/Installing+YouTrack+with+ZIP+Distribution and http://confluence.jetbrains.com/display/YTD6/Installing+YouTrack+with+JAR+Distribution .
That's more about preferences then advantages/disadvantages. Usually, admin person does this and the choice may depend on corporate policies or similar, self preferences, corporate software chain, are there any web servers above and etc.
Let me know if need any further assistance.