Soft reject, Help me please with this issue

I have received the following as soft reject points:

1. Any item in header/footer area that is a function should be moved into
   functions file. Otherwise theme might have issues when users overrides
   with custom templates via child theme.

here is our header code
http://ift.tt/1YGn7fB

here is footer code
http://ift.tt/1qYpdN1

can you please or any one explain how we can fix this or point out what the comment does it mean

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