If by user-defined checkstyle you mean that you have created several new rules and want them to be part of your style, you can do this as follows:
- Create a plugin project and add custom checks .
- Make the appropriate changes to plugin.xml , checkstyle_packages.xml.
- Export the project as Deployable plugins and fragments (export> Plugin development)
- Copy the flag file into the Eclipse Plugin folde, so you do not need to set your own validation.
You can reference this tutorial
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