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It doesn't immediately or easily answer the question: "what should I be working on right now, and in what exact order?" In order to make it do this I had to go write some custom SQL junk. I don't ever want to even look at custom SQL in a webapp. The whole point of an issue tracker is the answer this question.
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Its UI is clunky and the webapp is extremely slow (nearly 5 seconds to load the Dashboard).
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The keyboard shortcuts are a step in the right direction, but they're lacking. Look at Accunote to see how fast and efficient they could be.
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It lacks a decent CLI. I tried a few and they're either broken or extremely slow with aweful commands (reminds me of AWS) that would need to be wrapped in custom shell functions/alaises. I looked into the API to possibly create my own but it looked like some nasty SOAP crap.
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Creating and resolving bugs are probably the two most common things developers use JIRA for, so the UX needs to be heavily optimized to remove all the repetitive actions:
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When I resolve an issue, I assign it to the same person every time.
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When creating an issue I have to repeatedly fill out the same information (release, component, labels, assign to me). Would make more sense to just allow defaults.
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The plugins system is a confusing mess. I tried integrating with bitbucket for commit message integration and even followed some blogs on how to set it up (which should not be necessary). I think it worked eventually but I'm not sure why. Integrating with GitHub was actually easier, which is sad since bitbucket is made by the same company as JIRA.
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The docs don't seem to actually correspond with the product. For example, the nav menus mentioned here don't exist in my account: http://confluence.atlassian.com/display/JIRASTUDIO/Configuring+Commit+Commands+for+Issues
To put it another way: simplicity wins, and JIRA is anything but simple. Look at GitHub Issues to see how simple (and still powerful) task management could be. These are a few of the main issues that bug me, but it's hard to capture all the reasons. Using it makes me feel frustrated and inefficient.