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This fixes#2193, an issue that meant bit clears in PMP related CSRs
didn't immediately apply to an instruction already in the fetch stage
due to a lack of a pipeline flush.
With this change the pipeline will flush in that scenario, fixing the
issue. It now flushes the pipeline on all CSR modifications as this
makes the pipeline more resliant against similar issues in the future
(where the list of CSRs to flush on should have been updated but
wasn't).
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