update submodule documentation

INSTRUCTIONS.md

@@ -22,10 +22,16 @@ A list of required software to start developing a new task can be found in the [
 
 ### `common` submodule
 
-Initialize the `common` submodule by running the following command:
+If the submodule does not show any files, you will need to initialize the `common` submodule by running the following command:
 
 ```bash
-scripts/init_submodule.sh
+git submodule update --init --recursive
+```
+
+To update the repository with the latest changes from in the submodule, you can run the following command:
+
+```bash
+git pull --recurse-submodules
 ```
 
 ## Resources

README.md

@@ -20,6 +20,15 @@ The instructions below will guide you through creating a new repository from thi
 * Set the repository visibility to public.
 * Click "Create repository from template".
 
+## Clone the repository
+
+To clone the repository with the submodule files, you can use the following command:
+
+```bash
+git clone --recurse-submodules [email protected]:openproblems-bio/<repo_name>.git
+```
+
+
 ## What to do next
 
 Check out the [instructions](INSTRUCTIONS.md) for more information on how to update the example files and components. These instructions also contain information on how to build out the task and basic commands.