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Onyx works with repositories you already own. It does not scaffold a new repository or move your code out of git.

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Start with the GitHub App

1

Open the app

Go to app.onyxresearch.ai and sign in.
2

Connect GitHub

Install or manage the Onyx GitHub App for the GitHub account or organization.
3

Choose a repository

Grant Onyx access to the repository. Onyx records repository metadata and syncs the default branch head when the first branch syncs.
4

Create the branch

Use /onyx ... or onyx branch create from the local checkout. Pass --project-path when the research work is scoped to a subdirectory.
The GitHub App is used for repository selection, private repository access, installation metadata, webhook updates, repository sync, and code reads. Onyx does not store GitHub installation tokens. Internal project rows are created or reused automatically from branch creation.

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Choose a Project Path

Set projectPath when only a subdirectory belongs to the research work. Examples:
Repository layoutProject path
Whole repository""
App inside a monorepoapps/controller
Library packagepackages/planner
Paths returned by the app are relative to projectPath, while GitHub code reads still happen against the full repository.

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Sync Behavior

GitHub webhooks mark projects not_synced and schedule repository sync. The exact source of code remains git, and file trees, blobs, and diffs are read from actual commits through GitHub. To request a refresh manually: 
onyx sync
Or in the app, use the repository sync action for the tracked project.