We all know that nanoTime has problems. Many (most?) users of nanoTime, especially for benchmarking or concurrent algorithms, don't really care about the monotonicity guarantee and just want a "best-effort" "as-efficient-as-possible" version of nanoTime. Sure, some algorithms in java.util.concurrent might need to change slightly to accommodate nanoTime going backwards, but we already do this to some extent.
http://shipilev.net/blog/2014/nanotrusting-nanotime/ Some users have already created such a private nanoTime.
