[FIX] Update README links to user guide in docs (#95)

* update README links

* remove unneeded link to old docs page in setup script

README.md

@@ -9,7 +9,7 @@ Configuration files for a Neurobagel deployment.
 </div>
 
 ## How to use
-For detailed instructions on deploying Neurobagel for your use case, see the official Neurobagel documentation on [setting up a local knowledge graph (node)](https://neurobagel.org/getting_started/) and [configuration options](https://neurobagel.org/config/).
+For detailed instructions on deploying Neurobagel for your use case, see the official Neurobagel documentation on [setting up a local knowledge graph (node)](https://neurobagel.org/user_guide/getting_started/) and [configuration options](https://neurobagel.org/user_guide/config/).
 
 ### Using the full-stack Docker Compose file
 
@@ -26,7 +26,7 @@ For detailed instructions on deploying Neurobagel for your use case, see the off
     cp local_nb_nodes.template.json local_nb_nodes.json
     ```
 
-    Ensure to edit the [configuration file(s)](https://neurobagel.org/config/) according to your deployment.
+    Ensure to edit the [configuration file(s)](https://neurobagel.org/user_guide/config/) according to your deployment.
     **We strongly recommend changing the default passwords for your GraphDB instance, which are set using `NB_GRAPH_ADMIN_PASSWORD.txt` and `NB_GRAPH_PASSWORD.txt` in the ./secrets subdirectory by default.**
 
     :warning: **Note**: You **must** change the value of the `NB_API_QUERY_URL` variable in the `.env` file before you can launch any service stack that includes a query tool (i.e., `full_stack`, `local_federation`). 

scripts/graphdb_setup.sh

@@ -3,7 +3,7 @@
 # ARG_POSITIONAL_SINGLE([admin-pass],[Password for the "admin" superuser that GraphDB creates. If running the first-time user setup, this will be the password set for the admin. The admin user will only be used to create and modify permissions of other database users.])
 # ARG_OPTIONAL_SINGLE([env-file-path],[],[Path to a .env file containing environment variables for Neurobagel node configuration.],[.env])
 # ARG_OPTIONAL_BOOLEAN([run-user-setup],[],[Whether or not to run the first-time GraphDB setup steps, including changing the admin password and creating a new database user.],[on])
-# ARG_HELP([Run first-time user setup for a new GraphDB instance and/or set up a new GraphDB graph database. This script will automatically create a GraphDB configuration file (data-config.ttl) for your newly created database in your current directory. For more information, see https://neurobagel.org/infrastructure/.])
+# ARG_HELP([Run first-time user setup for a new GraphDB instance and/or set up a new GraphDB graph database. This script will automatically create a GraphDB configuration file (data-config.ttl) for your newly created database in your current directory.])
 # ARGBASH_GO()
 # needed because of Argbash --> m4_ignore([
 ### START OF CODE GENERATED BY Argbash v2.9.0 one line above ###
@@ -37,7 +37,7 @@ _arg_run_user_setup="on"
 
 print_help()
 {
-	printf '%s\n' "Run first-time user setup for a new GraphDB instance and/or set up a new GraphDB graph database. This script will automatically create a GraphDB configuration file (data-config.ttl) for your newly created database in your current directory. For more information, see https://neurobagel.org/infrastructure/."
+	printf '%s\n' "Run first-time user setup for a new GraphDB instance and/or set up a new GraphDB graph database. This script will automatically create a GraphDB configuration file (data-config.ttl) for your newly created database in your current directory."
 	printf 'Usage: %s [--env-file-path <arg>] [--(no-)run-user-setup] [-h|--help] <admin-pass>\n' "$0"
 	printf '\t%s\n' "<admin-pass>: Password for the \"admin\" superuser that GraphDB creates. If running the first-time user setup, this will be the password set for the admin. The admin user will only be used to create and modify permissions of other database users."
 	printf '\t%s\n' "--env-file-path: Path to a .env file containing environment variables for Neurobagel node configuration. (default: '.env')"