The recommendation depends entirely on your requirements.
Standalone is great for getting you started on any system, and remains excellent if you do not have any need to customise it.
As soon as you want to do anything clever, you should move to the WAR version. Bigger organisations use different application servers (e.g. the Tomcat bundled into Standalone is very rarely the "right" one, and a lot of organisations don't use Tomcat), and often customise stuff in Jira down at an application/code level (such as the authentication). It's far more easy to build a WAR with a few tweaks and deploy to a standardised container from the WAR install. Trying to do that with a Standalone is a nightmare.
I've never actually found a standalone version being used on any medium or large site. I've deployed it in a couple of small sites who really do need nothing more, and I use it for knocking up quick dev/test/demo systems. But I'd hazard a guess that most of Atlassian's users are using the WAR version. (Users by number of accounts, not installations)
Thanks for the clarification.
1. Understood that if we want to use different app server we should use war version.
Not clear on:
1. Authentication: We can connect to LDAP or other forms of authentication using stand alone, what is that stand alone cannot do that ear/war does in this aspect.
2. Customize JIRA: So if we want to change page look and feel or UI components is it better to use ear/war? Do you mean that users will build ear/war and deploy, instead of using the pre-built one?
I want to be able to decide which one to use ear/war or standalone, I do not find anywhere criteria that help me decide (you clarified couple, but looking to get better understanding.)
Please let me know.
There's still no easy answer to that. You need EAR/WAR as soon as you want to run it on a non-standalone application server, so that's an easy decision, but then it gets harder.
Your LDAP won't matter, I was using authentication as an example of one thing you might consider moving to WAR for (there's no way I'd try to bodge my current clients authentication into standalone...).
I'd start by examining how you use Jira now - is there stuff you really need to do that you can't at the moment (and can't be done with plugins?). If it's all working for you, then stick to standalone.
Worst case - start with standalone and work with it until you've got a good reason to change - the two setups are compatible!
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