Improve docs to encourage using secrets (#3272)

* Improved docs

* Update docs/book/how-to/project-setup-and-management/setting-up-a-project-repository/connect-your-git-repository.md

Co-authored-by: hyperlint-ai[bot] <154288675+hyperlint-ai[bot]@users.noreply.github.com>

---------

Co-authored-by: hyperlint-ai[bot] <154288675+hyperlint-ai[bot]@users.noreply.github.com>

docs/book/how-to/project-setup-and-management/setting-up-a-project-repository/connect-your-git-repository.md

@@ -54,6 +54,21 @@ zenml code-repository register <NAME> --type=github \
 
 where \<REPOSITORY> is the name of the code repository you are registering, \<OWNER> is the owner of the repository, \<NAME> is the name of the repository, \<GITHUB\_TOKEN> is your GitHub Personal Access Token and \<GITHUB\_URL> is the URL of the GitHub instance which defaults to `https://github.com.` You will need to set a URL if you are using GitHub Enterprise.
 
+{% hint style="warning" %}
+Please refer to the section on using secrets for stack configuration in order to securely store your GitHub 
+Personal Access Token.
+
+```shell
+# Using central secrets management
+zenml secret create github_secret \
+    --pa_token=<GITHUB_TOKEN>
+
+# Then reference the username and password
+zenml code-repository register ... --token={{github_secret.pa_token}}
+    ...
+```
+{% endhint %}
+
 After registering the GitHub code repository, ZenML will automatically detect if your source files are being tracked by GitHub and store the commit hash for each pipeline run.
 
 <details>
@@ -96,6 +111,21 @@ zenml code-repository register <NAME> --type=gitlab \
 
 where `<NAME>` is the name of the code repository you are registering, `<GROUP>` is the group of the project, `<PROJECT>` is the name of the project, \<GITLAB\_TOKEN> is your GitLab Personal Access Token, and \<GITLAB\_URL> is the URL of the GitLab instance which defaults to `https://gitlab.com.` You will need to set a URL if you have a self-hosted GitLab instance.
 
+{% hint style="warning" %}
+Please refer to the section on using secrets for stack configuration in order to securely store your GitLab
+Personal Access Token.
+
+```shell
+# Using central secrets management
+zenml secret create gitlab_secret \
+    --pa_token=<GITLAB_TOKEN>
+
+# Then reference the username and password
+zenml code-repository register ... --token={{gitlab_secret.pa_token}}
+    ...
+```
+{% endhint %}
+
 After registering the GitLab code repository, ZenML will automatically detect if your source files are being tracked by GitLab and store the commit hash for each pipeline run.
 
 <details>