Clang was writing paths to the dependency file that don't exist when using a sysroot with symlinks, causing everything to get rebuilt every time. This is reproducible on Linux by creating a symlink to '/', using that as the sysroot, and trying to build something with ninja that includes the C++ stdlib (e.g. a typical build of LLVM).
This fixes https://github.com/ninja-build/ninja/issues/1330 and somewhat matches gcc.
gcc canonicalizes system headers in dependency files under a -f[no-]canonical-system-headers, but it makes more sense to look at -canonical-prefixes.
D37954 was a previous attempt at this.