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Use Dashboard > Repositories to choose the GitHub repositories that Boxes should clone. Selected repositories are cloned when a Box starts. On the hosted Box image, the SSH user is user and the work directory is /home/user, so a selected repository is available at: 
/home/user/<repository-name>
Box uses the GitHub repository name for the folder, not the owner/name pair. For example:
GitHub repoBox path
ariana-dot-dev/ariana-ide-private/home/user/ariana-ide-private
octocat/hello-world/home/user/hello-world
If a Box has one selected repository, Box uses that repository folder as the main project directory for agent tools. If a Box has multiple selected repositories, /home/user stays the parent workspace and each repository is a sibling folder.

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Branches

Each selected repository has a base branch. Box clones that branch first. Box does not create a new branch automatically, including for forked Boxes. Repositories stay on the configured base branch unless you or a command inside the Box changes branches.

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Secret Files

Secret file paths in Dashboard > Secrets are relative to the Box work directory, /home/user. The secrets dashboard does not have a repository selector, so include the repository folder name when you want to write inside a selected repository. For example, if you selected ariana-dot-dev/ariana-ide-private and want to create .env under its backend folder, use: 
ariana-ide-private/backend/.env
That creates: 
/home/user/ariana-ide-private/backend/.env