In development of 3.0, Sphinx starts to obey to the rule of
"Identifier Normalization" of docutils.  This extends it to allow
dots(".") and underscores("_") for node identifier.

It allows Sphinx to generate node identifier from source string as
possible as it is (bacause dots and underscores are usually used in
many programming langauges).

This change will keep not to break hyperlinks as possible.

In Python 3, the default encoding of source files is utf-8. The encoding
cookie is now unnecessary and redundant so remove it. For more details,
see the docs:

https://docs.python.org/3/howto/unicode.html#the-string-type

> The default encoding for Python source code is UTF-8, so you can
> simply include a Unicode character in a string literal ...

Includes a fix for the flake8 header checks to stop expecting an
encoding cookie.