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To resolve jar conflicts in my application, I use the shaded plugin's relocation feature. It works for me, but i feel it is a hack. I would like to understand the downsides of using the relocation feature if any.
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The main issue is that it can fail in cases where the package name is directly defined (not just imported). For example, if you are using reflection and instantiating the a class by its name (including the package name) it will generate the wrong one. Similar problems can occur when the the package is defined in a manifest (there is a transformer for that). See the plugin info for more information.
Another place where this could be an issue is with a third party dependency which uses the same dependency. Consider for example package A which is provided. If package A depends on the relocated package it will in the run time use the provided instance instead of the relocated one. This can lead to unforeseen effects.
An additional issue is that in some cases, the package may contain some initialized/static information (e.g. it downloads some info once or has some big static table). In these cases it is important to understand that there are now TWO completely separate instances of the package.