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Both fixes are good calls, dotfile-sync portability and the symlink-clobber bug are real annoyances. Two questions before merge:
Does Claude Code's hook runner actually expand ${HOME} when it spawns the command, or does it pass the string straight through? If it's the latter, the hook will silently fail to fire after this change. A quick echo test on a fresh install would confirm. Worth a line in the README either way so users know the entry is intentionally unexpanded.
readlink -f is GNU-flavored and only landed in macOS 12.3. Probably fine given the project's macOS focus, but a portable alternative (cd "$(dirname "$SETTINGS")" && pwd -P, or python3 -c 'import os,sys;print(os.path.realpath(sys.argv[1]))' "$SETTINGS") would avoid a surprise on older systems.
Otherwise lgtm, this is a clean fix.
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${HOME}instead of full path to ensure settings can be shared across different machines.settings.jsonsymlink, if settings.json is a symlink.