Implement workaround for symlink problem

As in https://bugs.eclipse.org/bugs/show_bug.cgi?id=354367 and
https://git.eclipse.org/r/#/c/9379/, JGit has no compatibility
with git about symlink handling.

JGit tries to handle symlinks as a copy of original files, but git
keeps them as they are.

This patch ignores symlink difference in worktree clean detection.