If all your doctypes are custom ones and included in the custom app then just do bench build and bench migrate.
If your customizations are for standard doctypes and written in client script, then you got to use fixtures in the hooks file to export them to the app.
fixtures = [
{
"doctype": "Client Script",
"filters" : [
"name",
"in",
[
'name_of_client_Scipt'
]
]
}
]