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It sounds like you need some more specialized queries. I'm not fully familar with what you're doing, but it sounds like you built queries into the datastructure, whereas I tend to keep queries out of the datastructure. I have utility classes build the datastructure I need. For instance, should I want to perform a specific task (such as get an issue history), I'd write a method getIssueHistory(), pass it all the variables I'd need, and form the whole query right there, if possible.
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