Document CLI Utility Commands

Document some CLI utility commands useful for development and for supporting
the operation of the GN3 app.

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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
+```
+
+## 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
+```