JIRA definitely enables one to lose track of the big picture. It starts off by being DIS-integrative: exploding things into atoms.
Then, as the next layer, it allows you to build an integrated picture through the use of classifiers: Labels, Components, Fix-Versions and so on. And, ... classification is hard.
One aspect of a detailed breakdown is that one may end up with (story-points or other) estimates at a very low level of detail: too low a level. When you add across JIRAs you might end up with twice what you ought to spend, because you picked up the same artifact 4 times, in 4 different sprints, even though you did have visibility to all 4 changes at the start.
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