add-empty-folders.lua

-- Using luvit.io and https://github.com/creationix/lua-git

local makeChroot = require('coro-fs').chroot
local mount = require('git').mount

coroutine.wrap(function ()
    local db = mount(makeChroot(".git"))

    local head = db.getHead()
    local commit = db.loadAs("commit", head)
    local tree = db.loadAs("tree", commit.tree)

    local hasConfig = false
    local hasHooks = false
    for _,entry in pairs(tree) do
        if entry.name == 'config' then hasConfig = true end
        if entry.name == 'hooks' then hasHooks = true end
    end
    
    local empty = db.saveAs('tree', {})

    if not hasConfig then
        print "Adding empty config folder"
        tree[#tree+1] = {hash = empty, name = 'config', mode = 16384}
    end
    if not hasHooks then
        print "Adding empty hooks folder"
        tree[#tree+1] = {hash = empty, name = 'hooks', mode = 16384}
    end

    local newTree = db.saveAs('tree', tree)
    commit.tree = newTree
    local newCommit = db.saveAs('commit', commit)
    p("original commit", head)
    p("new commit", newCommit)

end)()

You can see the generated commit and tree by passing the hash to git cat-file -p

$ git cat-file -p 754ae8c8361c8b09141c757f22050602334ee96c
040000 tree 4b825dc642cb6eb9a060e54bf8d69288fbee4904    config
040000 tree 4b825dc642cb6eb9a060e54bf8d69288fbee4904    hooks
040000 tree cc41d02fab43d45d5405f1a1dcec0bd432da0123    profiles
100644 blob 8725d157a96c48e0c50c0f544b634e365bc11a99    remotes.txt
100644 blob 60f89a501ab6988e2c42f5d37c325bd43eadc80a    settings.yml

Then if you like it, move the current branch to the new commit with a hard reset.