Code:play 

package main

import (
	"context"
	"errors"
	"fmt"
	"log"

	"github.com/bep/simplecobra"
)

func main() {
	rootCmd := &rootCommand{name: "root",
		commands: []simplecobra.Commander{
			&lvl1Command{name: "foo"},
			&lvl1Command{name: "bar",
				commands: []simplecobra.Commander{
					&lvl2Command{name: "baz"},
				},
			},
		},
	}

	x, err := simplecobra.New(rootCmd)
	if err != nil {
		log.Fatal(err)
	}
	cd, err := x.Execute(context.Background(), []string{"bar", "baz", "--localFlagName", "baz_local", "--persistentFlagName", "baz_persistent"})
	if err != nil {
		log.Fatal(err)
	}

	// These are wired up in Init().
	lvl2 := cd.Command.(*lvl2Command)
	lvl1 := lvl2.parentCmd
	root := lvl1.rootCmd

	fmt.Printf("Executed %s.%s.%s with localFlagName %s and and persistentFlagName %s.\n", root.name, lvl1.name, lvl2.name, lvl2.localFlagName, root.persistentFlagName)
}

type rootCommand struct {
	name   string
	isInit bool

	persistentFlagName string
	localFlagName      string

	persistentFlagNameC string
	localFlagNameC      string

	ctx                  context.Context
	initThis             *simplecobra.Commandeer
	initRunner           *simplecobra.Commandeer
	failWithCobraCommand bool
	failRun              bool

	commands []simplecobra.Commander
}

func (c *rootCommand) Commands() []simplecobra.Commander {
	return c.commands
}

func (c *rootCommand) PreRun(this, runner *simplecobra.Commandeer) error {
	c.isInit = true
	c.persistentFlagNameC = c.persistentFlagName + "_rootCommand_compiled"
	c.localFlagNameC = c.localFlagName + "_rootCommand_compiled"
	c.initThis = this
	c.initRunner = runner
	return nil
}

func (c *rootCommand) Name() string {
	return c.name
}

func (c *rootCommand) Run(ctx context.Context, cd *simplecobra.Commandeer, args []string) error {
	if c.failRun {
		return errors.New("failRun")
	}
	c.ctx = ctx
	return nil
}

func (c *rootCommand) Init(cd *simplecobra.Commandeer) error {
	if c.failWithCobraCommand {
		return errors.New("failWithCobraCommand")
	}
	cmd := cd.CobraCommand
	localFlags := cmd.Flags()
	persistentFlags := cmd.PersistentFlags()

	localFlags.StringVar(&c.localFlagName, "localFlagName", "", "set localFlagName")
	persistentFlags.StringVar(&c.persistentFlagName, "persistentFlagName", "", "set persistentFlagName")

	return nil
}

type lvl1Command struct {
	name   string
	isInit bool

	aliases []string

	localFlagName  string
	localFlagNameC string

	failInit             bool
	failWithCobraCommand bool
	disableSuggestions   bool

	rootCmd *rootCommand

	commands []simplecobra.Commander

	ctx context.Context
}

func (c *lvl1Command) Commands() []simplecobra.Commander {
	return c.commands
}

func (c *lvl1Command) PreRun(this, runner *simplecobra.Commandeer) error {
	if c.failInit {
		return fmt.Errorf("failInit")
	}
	c.isInit = true
	c.localFlagNameC = c.localFlagName + "_lvl1Command_compiled"
	c.rootCmd = this.Root.Command.(*rootCommand)
	return nil
}

func (c *lvl1Command) Name() string {
	return c.name
}

func (c *lvl1Command) Run(ctx context.Context, cd *simplecobra.Commandeer, args []string) error {
	c.ctx = ctx
	return nil
}

func (c *lvl1Command) Init(cd *simplecobra.Commandeer) error {
	if c.failWithCobraCommand {
		return errors.New("failWithCobraCommand")
	}
	cmd := cd.CobraCommand
	cmd.DisableSuggestions = c.disableSuggestions
	cmd.Aliases = c.aliases
	localFlags := cmd.Flags()
	localFlags.StringVar(&c.localFlagName, "localFlagName", "", "set localFlagName for lvl1Command")
	return nil
}

type lvl2Command struct {
	name          string
	isInit        bool
	localFlagName string

	ctx       context.Context
	rootCmd   *rootCommand
	parentCmd *lvl1Command
}

func (c *lvl2Command) Commands() []simplecobra.Commander {
	return nil
}

func (c *lvl2Command) PreRun(this, runner *simplecobra.Commandeer) error {
	c.isInit = true
	c.rootCmd = this.Root.Command.(*rootCommand)
	c.parentCmd = this.Parent.Command.(*lvl1Command)
	return nil
}

func (c *lvl2Command) Name() string {
	return c.name
}

func (c *lvl2Command) Run(ctx context.Context, cd *simplecobra.Commandeer, args []string) error {
	c.ctx = ctx
	return nil
}

func (c *lvl2Command) Init(cd *simplecobra.Commandeer) error {
	cmd := cd.CobraCommand
	localFlags := cmd.Flags()
	localFlags.StringVar(&c.localFlagName, "localFlagName", "", "set localFlagName for lvl2Command")
	return nil
}

Output:

Executed root.bar.baz with localFlagName baz_local and and persistentFlagName baz_persistent.