dbewedb

list = [
    warehouses: [1]
,
    warehouses: [2]
,
    warehouses: [3]
,
    warehouses: [4, 1]
,
    warehouses: [5, 2]
,
    warehouses: [6, 3, 2]
]

#получаем массив id магазинов отсортированный по частоте
counted = list
    .reduce (acc, {warehouses}) ->
        for w in warehouses
            acc[w] = {warehouse: w, data: []} unless acc[w]
            acc[w].data.push w
        acc
     , []
     .sort (a, b) -> b.data.length - a.data.length
     .map (i) -> i.warehouse
     .filter (i) -> i > 0

_r = []

for w in counted
     _r[w] = {warehouse: w, data: []} unless _r[w]
     for i in list
         if i.warehouses.includes w
             _r[w].data.push i
             delete list[i]

result = _r
    .sort (a, b) -> b.data.length - a.data.length
    .filter (i) -> i isnt null

console.log 'r', result