Script for syncing all folders with .sync file (tested only on MacOS with brew rsync)

sync_by_dot_sync.sh

#!/usr/bin/env bash
set -euo pipefail

RSYNC_CMD="/opt/homebrew/bin/rsync"

# Usage: sync_by_dot_sync.sh [--skip-missing-check] SOURCE_DIR DEST_DIR
# Finds top-level folders (w.r.t. source) that contain a file named ".sync"
# (ignoring any folder that is a subfolder of another .sync folder),
# checks for files that exist only on destination (warns / lists them),
# prompts to continue, and then rsyncs each selected folder WITHOUT deleting destination-only files.
#
# Behavior:
#   * If missing files are found and --skip-missing-check is NOT given, the script prints a grouped
#     list of destination-only files and prompts once for whether to continue the sync.
#   * If the user answers 'y' or 'Y', syncing proceeds. Any other answer aborts.
#   * Actual rsync does not use --delete; it copies/upates files from source to destination only.

PRINT_USAGE() {
  cat <<EOF
Usage: $0 [--skip-missing-check] [--rsync-opts "OPTS"] SOURCE_DIR DEST_DIR

Options:
  --skip-missing-check   Skip checking for destination-only files (and skip the prompt).
  --rsync-opts "OPTS"      Extra options passed verbatim to rsync
                           Example: --rsync-opts "--exclude=.git --numeric-ids"
EOF
}

# parse args

SKIP_MISSING_CHECK=false
RSYNC_EXTRA_OPTS=()

while [ "$#" -gt 0 ]; do
  case "$1" in
    --skip-missing-check)
      SKIP_MISSING_CHECK=true
      shift
      ;;
    --rsync-opts)
      [ "$#" -lt 2 ] && { PRINT_USAGE >&2; exit 1; }
      RSYNC_EXTRA_OPTS=$($2)
      shift 2
      ;;
    --*)
      PRINT_USAGE >&2
      exit 1
      ;;
    *)
      break
      ;;
  esac
done

[ "$#" -ne 2 ] && { PRINT_USAGE >&2; exit 1; }

SOURCE="$1"
DEST="$2"

if [ ! -d "$SOURCE" ]; then
  echo "Source directory does not exist: $SOURCE" >&2
  exit 2
fi

mkdir -p "$DEST"
SOURCE="$(cd "$SOURCE" && pwd -P)"
DEST="$(cd "$DEST" && pwd -P)"

echo "Finding folders to sync under: $SOURCE"
echo "Syncing to: $DEST"
echo

# collect candidate directories that contain .sync
candidates=()
while IFS= read -r -d '' f; do
  dir="$(cd "$(dirname "$f")" && pwd -P)"
  candidates+=("$dir")
done < <(find "$SOURCE" -type f -name '.sync' -print0)

# nothing to do
if [ "${#candidates[@]}" -eq 0 ]; then
  echo No folders found for syncing
  exit 0
fi

# deduplicate and sort by path length (shorter first so parents come before children)
IFS=$'\n' sorted_unique=($(printf "%s\n" "${candidates[@]}" \
  | awk '!seen[$0]++' \
  | sed 's:/*$::' \
  | awk '{ print length, $0 }' \
  | sort -n \
  | cut -d' ' -f2-))

# select only top-level .sync dirs (exclude those inside previously selected dirs)
selected=()
for dir in "${sorted_unique[@]}"; do
  skip=false
  if [[ -n ${selected:-} ]]; then
    for sel in "${selected[@]}"; do
      case "$dir" in
        "$sel"|"$sel"/*) skip=true; break ;;
      esac
    done
  fi
  if [ "$skip" = false ]; then
    selected+=("$dir")
  fi
done

if [ "${#selected[@]}" -gt 0 ]; then
  echo "Selected folders:"
  for dir in "${selected[@]}"; do
    echo "  $dir"
  done
  echo
else
  echo "No folders with .sync found"
  exit 0
fi

echo "Syncing folders:"
for dir in "${selected[@]}"; do
  if [ "$dir" = "$SOURCE" ]; then
    rel="."
  else
    rel="${dir#$SOURCE/}"
  fi
  echo "  $SOURCE/$rel  ->  $DEST/$rel"
done

echo
echo "Total folders: ${#selected[@]}"
echo

RSYNC_BASE_OPTS=(-av)
DELETE_MODE=""   # empty or --delete

# Check for destination-only (would be deleted) files, collect by relative folder
missing_map=()
any_missing=false

# missing-file check and decision
if [ "$SKIP_MISSING_CHECK" = false ]; then
  any_missing=false

  echo "Finding files that exist in target but not in source..."
  for dir in "${selected[@]}"; do
    echo "${dir}"
    rel="${dir#$SOURCE/}"
    [ "$dir" = "$SOURCE" ] && rel="."
    target="$DEST/$rel"
    mkdir -p "$target"
    OPTS=( "${RSYNC_BASE_OPTS[@]}" )
    if [ "${#RSYNC_EXTRA_OPTS[@]}" -gt 0 ]; then
      OPTS+=( "${RSYNC_EXTRA_OPTS[@]}" )
    fi
    OPTS+=(--dry-run --delete "${dir}/" "${target}/")

    dry=$("${RSYNC_CMD}" "${OPTS[@]}") #2>/dev/null || true)"
    deletes="$(printf '%s\n' "$dry" | awk '/^deleting / { sub(/^deleting /,""); print }')"

    if [ -n "$deletes" ]; then
      any_missing=true
      missing_map["$rel"]="$deletes"
    fi
  done

  if [ "$any_missing" = true ]; then
    echo "Destination-only files detected:" >&2
    for rel in "${!missing_map[@]}"; do
      echo "[$rel]" >&2
      printf '%s\n' "${missing_map[$rel]}" | sed 's/^/  /' >&2
    done

    printf "Choose action: (d)elete and sync / (k)eep and sync / (q)uit: " >&2
    IFS= read -r choice
    case "$choice" in
      d|D) DELETE_MODE="--delete" ;;
      k|K) DELETE_MODE="" ;;
      q|Q) exit 0 ;;
      *) exit 0 ;;
    esac
  fi
fi

echo
echo "Performing sync"
# perform sync
for dir in "${selected[@]}"; do
  echo
  echo "Syncing ${dir}"
  rel="${dir#$SOURCE/}"
  [ "$dir" = "$SOURCE" ] && rel="."
  target="$DEST/$rel"
  mkdir -p "$target"
  OPTS=( "${RSYNC_BASE_OPTS[@]}" ${DELETE_MODE} )
  if [ "${#RSYNC_EXTRA_OPTS[@]}" -gt 0 ]; then
    OPTS+=( "${RSYNC_EXTRA_OPTS[@]}")
  fi
  OPTS+=( "${dir}/" "${target}/" )

  "${RSYNC_CMD}" "${OPTS[@]}"
done