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/usr/sbin/waagent is in walinuxagent 2.2.32-0ubuntu1~16.04.2.

This file is owned by root:root, with mode 0o755.

The actual contents of the file can be viewed below.

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#! /usr/bin/env python3
#
# Azure Linux Agent
#
# Copyright 2015 Microsoft Corporation
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
#     http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
#
# Requires Python 2.6 and Openssl 1.0+
#
# Implements parts of RFC 2131, 1541, 1497 and
# http://msdn.microsoft.com/en-us/library/cc227282%28PROT.10%29.aspx
# http://msdn.microsoft.com/en-us/library/cc227259%28PROT.13%29.aspx
#

import os
import imp
import sys

if __name__ == '__main__' :
    import azurelinuxagent.agent as agent
    """
    Invoke main method of agent
    """
    agent.main()

if __name__ == 'waagent':
    """
    Load waagent2.0 to support old version of extensions
    """
    if sys.version_info[0] == 3:
        raise ImportError("waagent2.0 doesn't support python3")
    bin_path = os.path.dirname(os.path.abspath(__file__))
    agent20_path = os.path.join(bin_path, "waagent2.0")
    if not os.path.isfile(agent20_path):
        raise ImportError("Can't load waagent")
    agent20 = imp.load_source('waagent', agent20_path)
    __all__ = dir(agent20)