Security gap: Team members can use GitHub App private keys to bypass repo access restrictions

[erel-ironalgo]

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Bug

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Summary

There is currently a security gap when using GitHub Apps in an organization with multiple repositories and restricted access.

Scenario:

• We have a GitHub organization with two repositories:
  • Repo A: shared with all team members.
  • Repo B: restricted, only approved members have access.
• We also have a GitHub App that grants read access to Repo B.
• Team members are allowed to create and manage GitHub Apps at the organization level.

Problem

Even if a user does not have access to Repo B, they can:

1. Configure or manage the GitHub App that has access to Repo B.
2. Generate a new private key for the app.
3. Use this private key to clone Repo B’s contents.

This effectively bypasses repository-level access control and exposes sensitive data.

Why this is severe

• It breaks the security model of repository permissions.
• It allows unauthorized users to escalate privileges by exploiting GitHub App private keys.
• Organization owners currently have no way to restrict which GitHub Apps a user can configure.

Desired Behavior

To resolve this, one of the following mechanisms should exist:

1. User-bound private keys for GitHub Apps

   • Private keys generated for a GitHub App should be tied to the user’s own repo/org permissions.
   • If the user does not have access to Repo B, their generated private key should not allow them to access Repo B through the app.

2. Granular permissions for GitHub App management

   • By default, block all GitHub Apps from being managed by team members.
   • Organization owners can then explicitly whitelist specific apps per team or user.
   • This ensures that only approved users can configure or regenerate private keys for sensitive apps (e.g., the app that grants Repo B access).

Impact

This issue allows any team member with GitHub App management rights to circumvent repository restrictions, creating a critical security risk for organizations with tiered repository access.

Request

• Provide a mechanism to enforce repository permissions when using GitHub App private keys, or
• Allow organization owners to control which GitHub Apps team members can configure/manage.

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