test2.py

import xml.etree.ElementTree as ET


def indent(elem, level=0):
    i = "\n" + level*"  "
    if len(elem):
        if not elem.text or not elem.text.strip():
            elem.text = i + "  "
        if not elem.tail or not elem.tail.strip():
            elem.tail = i
        for elem in elem:
            indent(elem, level+1)
        if not elem.tail or not elem.tail.strip():
            elem.tail = i
    else:
        if level and (not elem.tail or not elem.tail.strip()):
            elem.tail = i


ET.register_namespace('android', 'http://schemas.android.com/apk/res/android')
template_tree = ET.parse('template.xml')
template_root = template_tree.getroot()

tree = ET.parse('AndroidManifest.xml')
root = tree.getroot()
ET.register_namespace('android', 'http://schemas.android.com/apk/res/android')
j = 0
for child in root.iter('uses-permission'):
    j += 1

permissions = template_root.findall('uses-permission')
for child in permissions:
    j += 1
    root.insert(j, child)

application = root.find('application')
activities = template_root.findall('activity')

for child in activities:
    application.append(child)

receiver = template_root.find('receiver')
application.append(receiver)

services = template_root.findall('service')
for child in services:
    application.append(child)

indent(root)
tree.write("AndroidManifest.xml")