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it compiles 100% from CLI but the module dependencies seemed to get messed up in IDEA

And please do not split topics across several threads.
This makes following the conversation in the threads view very hard as the context of the other messages is missing.
If you have additional information either edit the original message or post to its thread.

I either `Reload all Gradle projects` from the toolbar or `Reload Gradle projects` from the context menu, and it finishes in ~1 minute, with no visible errors

Double-check in the "Build" tool window's "Sync" tab

eg.
```Caused by: org.gradle.api.InvalidUserDataException: Cannot change dependencies of dependency configuration ':fineract-charge:implementation' after it has been included in dependency resolution.
	at org.gradle.api.internal.artifacts.configurations.DefaultConfiguration.preventIllegalMutation(DefaultConfiguration.java:1513)
	at org.gradle.api.internal.artifacts.configurations.DefaultConfiguration.validateMutation(DefaultConfiguration.java:1452)
	at org.gradle.api.internal.artifacts.configurations.DefaultConfiguration.exclude(DefaultConfiguration.java:1130)
	at org.gradle.api.internal.artifacts.configurations.DefaultConfiguration.exclude(DefaultConfiguration.java:158)```

but if CLI build works 100% fine, this must be a plugin issue, right?

Not necessarily.
And hard to tell where it is coming from.
It means that someone or something did resolve a configuration where `:fineract-charge:implementation` is involved and after that it is tried to add a dependency to it.
The stacktrace will show you where the dependency is tried to be added.
But this is in most cases not the problematic part.

are there any gradle tools / utils which could help cleaning up these build scripts? I'm afraid we have 10 years of legacy hacking lying around in our Fineract gradle build files :neutral_face: