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Order of application of suggestions while using Jlanguagetool.check() API

I had written two custom grammar rules. Now when I am testing the rules(using the standalone Desktop version of LT) on an incorrect sentence, the rules are applied in the order in which they were written in the xml file. But when I used the Jlanguagetool API’s check function, it only returns the list of RuleMatches corresponding to the rule that was written later below in the xml file.
Can anyone confirm this?

There’s some filtering going on, for example with rules in the same rule group. To be more specific, we’d need to see your custom rules.