FLASK_APP, FLASK_ENV, and FLASK_DEBUG can be set with options to the flask CLI instead of requiring that they be set with env vars. They can still be set with env vars.

• -e, --env-file specifies an additional dotenv file to load, in addition to .env and .flaskenv. FLASK_SKIP_DOTENV does not skip this option, only the two default files. Did not add an option for FLASK_SKIP_DOTENV since it's only useful when being called from another CLI that already manages env vars and can set it already.
• -A, --app
• -E, --env works by setting the FLASK_ENV env var internally, as this is still the only way it can be available early enough during Flask.__init__ and factory functions without making it an argument to __init__.
• --debug/--no-debug only sets app.debug if it's actually provided on the command line, and works like --env by setting the FLASK_DEBUG env var. It is still skipped for now if ScriptInfo.set_debug_flag is False because I couldn't think of a good way to do that.

This did require some tricks to get custom commands to work. The app needs to be loaded as early as possible, otherwise --help and no_args_is_help won't see it in time to list the commands. And --env-file needs to be evaluated the earliest because it can set FLASK_APP. Both these options are is_eager=True, and also get processed before parse_args runs in case they were only given as env vars.

All docs are rewritten to use the CLI options instead of environment variables in most cases. Some areas still call out or show how to use environment variables.

fixes #2292
fixes #3108