Summary of changes in this PR:
- Refactor files involved in the `certbot` module to be of a similar structure to every other package; that is, inside a directory inside the main repo root (see below).
- Make repo root README symlink to `certbot` README.
- Pull tests outside of the distributed module.
- Make `certbot/tests` not be a module so that `certbot` isn't added to Python's path for module discovery.
- Remove `--pyargs` from test calls, and make sure to call tests from repo root since without `--pyargs`, `pytest` takes directory names rather than package names as arguments.
- Replace mentions of `.` with `certbot` when referring to packages to install, usually editably.
- Clean up some unused code around executing tests in a different directory.
- Create public shim around main and make that the entry point.

New directory structure summary:
```
repo root ("certbot", probably, but for clarity all files I mention are relative to here)
├── certbot
│   ├── setup.py
│   ├── certbot
│   │   ├── __init__.py
│   │   ├── achallenges.py
│   │   ├── _internal
│   │   │   ├── __init__.py
│   │   │   ├── account.py
│   │   │   ├── ...
│   │   ├── ...
│   ├── tests
│   │   ├── account_test.py
│   │   ├── display
│   │   │   ├── __init__.py
│   │   │   ├── ...
│   │   ├── ... # note no __init__.py at this level
│   ├── ...
├── acme
│   ├── ...
├── certbot-apache
│   ├── ...
├── ...
```

* refactor certbot/ and certbot/tests/ to use the same structure as the other packages

* git grep -lE "\-e(\s+)\." | xargs sed -i -E "s/\-e(\s+)\./-e certbot/g"

* git grep -lE "\.\[dev\]" | xargs sed -i -E "s/\.\[dev\]/certbot[dev]/g"

* git grep -lE "\.\[dev3\]" | xargs sed -i -E "s/\.\[dev3\]/certbot[dev3]/g"

* Remove replacement of certbot into . in install_and_test.py

* copy license back out to main folder

* remove linter_plugin.py and CONTRIBUTING.md from certbot/MANIFEST.in because these files are not under certbot/

* Move README back into main folder, and make the version inside certbot/ a symlink

* symlink certbot READMEs the other way around

* move testdata into the public api certbot zone

* update source_paths in tox.ini to certbot/certbot to find the right subfolder for tests

* certbot version has been bumped down a directory level

* make certbot tests directory not a package and import sibling as module

* Remove unused script cruft

* change . to certbot in test_sdists

* remove outdated comment referencing a command that doesn't work

* Install instructions should reference an existing file

* update file paths in Dockerfile

* some package named in tox.ini were manually specified, change those to certbot

* new directory format doesn't work easily with pyargs according to http://doc.pytest.org/en/latest/goodpractices.html#tests-as-part-of-application-code



* remove other instance of pyargs

* fix up some references in _release.sh by searching for ' . ' and manual check

* another stray . in tox.ini

* fix paths in tools/_release.sh

* Remove final --pyargs call, and now-unnecessary call to modules instead of local files, since that's fixed by certbot's code being one layer deeper

* Create public shim around main and make that the entry point

* without pyargs, tests cannot be run from an empty directory

* Remove cruft for running certbot directly from main

* Have main shim take real arg

* add docs/api file for main, and fix up main comment

* Update certbot/docs/install.rst

Co-Authored-By: Brad Warren <bmw@users.noreply.github.com>

* Fix comments in readthedocs requirements files to refer to current package

* Update .[docs] reference in contributing.rst

* Move plugins tests to certbot tests directory

* add certbot tests to MANIFEST.in so packagers can run python setup.py test

* move examples directory inside certbot/

* Move CHANGELOG into certbot, and create a top-level symlink

* Remove unused sys and logging from main shim

* nginx http01 test no longer relies on certbot plugins common test