the option onlyPlugins need rethinking

[BioPhoton]

The option onlyPlugins remove a whole category if 1 audit is included. This is no good DX as when debugging I want to see the category scores too. A potential solution could be just remove refs from a category, not the category it self.

blocked by #515 as it includes a helper function to filter refs in a category

[vmasek]

@BioPhoton please check if the category audits are still replaced or if they get merged. If the case is replacement, please update the issue

[hanna-skryl]

Since the issue was created, the filtering logic has been updated and centralized within a single filtering middleware function: #822 and #831.

The current behavior already matches what was requested: categories are kept, and only specific references within them are filtered out based on the onlyPlugins and skipPlugins options. The middleware uses the filterItemRefsBy helper function (introduced in #515) to filter references within a category, ensuring that categories remain intact while filtering only the relevant plugin references, providing the expected developer experience.