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As those synchronized methods are called at the start and the end of builds, I don't think they cause being slow.
Rather, changes to watch log outputs may cause the problem.
https://github.com/jenkinsci/build-timeout-plugin/commit/2129c5d8fc4a9d9432cf95ce34ce522e646eb3ff#diff-891dfa43e0d85dea7162d46b430299d7R184
I want to make some testing versions to identify the cause.
But I'm not sure how to reproduce the problem.
Can you try testing versions if I provide?