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-# CLI Utility Scripts
-
-This documents the various utility scripts that are provided with the project
-whose purposes are to support the operation of the application in one way or
-another.
-
-To get a list of the available scripts/flask commands that can be run, do:
-
-```sh
-FLASK_APP="main.py" flask --help
-```
-
-With that, you should get a list of commands, which as of 2023-05-26 are:
-
-```sh
-. . . output truncated to save space ...
-
-Commands:
-  apply-migrations     Apply the dabasase migrations.
-  assign-system-admin  Assign user with ID `user_id` administrator role.
-  init-dev-clients     Initialise a development client for OAuth2 sessions.
-  init-dev-users       Initialise development users for OAuth2 sessions.
-  routes               Show the routes for the app.
-  run                  Run a development server.
-  shell                Run a shell in the app context.
-```
-
-*NB*: You can simply do `export FLASK_APP="main.py"` at the beginning of your
-shell session and then just run the commands without prepending with the
-`FLASK_APP="main.py"` declaration.
-
-## Setting a User as System Administrator
-
-Once you have registered the user with the new (as of 2023-05-26)
-auth(entic|oris)ation system, you can then proceed to specify that the user is
-going to be a system administrator of the system.
-
-You will need to retrieve the users identifier (UUID) from the system; say the
-UUID you get for the user is `5b15ef01-a9d7-4ee4-9a38-fe9dd1d871b8`, you can
-then set that user as a system administrator by running:
-
-```sh
-FLASK_APP="main.py" flask assign-system-admin 5b15ef01-a9d7-4ee4-9a38-fe9dd1d871b8
-```
-
-You can retrieve the user ID from the (SQLite) database, with something like:
-
-```sh
-$ sqlite3 /home/frederick/genenetwork/gn3_files/db/auth.db
-SQLite version 3.40.0 2022-11-16 12:10:08
-Enter ".help" for usage hints.
-sqlite> SELECT * FROM users;
-0ad1917c-57da-46dc-b79e-c81c91e5b928|test@development.user|Test Development User
-9c5d4ddf-c361-4133-add3-9ab9845bb9f2|fredtest02@gmail.com|A New Group Member
-b4a8ed7a-a878-4884-94e0-26d3fe0c56a3|fredleader@gmail.com|Frederick the Group Leader
-```
-
-## Make Existing Data Publicly Visible
-
-This will only act on any existing data that is not already linked with a user
-group in the new auth system.
-
-This can be run using flask with
-
-```sh
-FLASK_APP="main.py" flask make-data-public
-```
-
-which will use the application's configuration settings for the
-auth(entic|oris)ation database and the MariaDB database.
-
-You could also run the script directly with:
-
-```sh
-python3 -m scripts.migrate_existing_data AUTHDBPATH MYSQLDBURI
-```
-
-where `AUTHDBPATH` and `MYSQLDBURI` are replaced with the appropriate values,
-e.g.
-
-```sh
-python3 -m scripts.migrate_existing_data \
-    /home/frederick/genenetwork/gn3_files/db/auth.db \
-    mysql://webqtlout:webqtlout@127.0.0.1:3307/db_webqtl
-```
-
-## List Available Routes
-
-```sh
-FLASK_APP="main.py" flask routes
-```
-
-## Drop Into a Python Shell
-
-```sh
-FLASK_APP="main.py" flask shell
-```
-
-## Development Scripts
-
-The commands in this section are meant for easing development and are not to be
-run in a production environment.
-
-### Setting up a Sample User for Development
-
-```sh
-FLASK_APP="main.py" flask init-dev-users
-```
-
-That will initialise your development database with a development user with the
-following details:
-
-- User ID: 0ad1917c-57da-46dc-b79e-c81c91e5b928
-- Email: test@development.user
-- Password: testpasswd
-
-### Setting up Sample OAuth2 Client for Development
-
-```sh
-FLASK_APP="main.py" flask init-dev-clients
-```