This question is in reference to Atlassian Documentation: Add Users, Set Permissions, and Review Account Plans
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You cannot. Project level and repo level permissions are additive. Repo permissions do not override project-level permissions.
If you have a repo in a project that you don't want someone with project-level permissions to access, move it to a new project.
You can, of course, prevent them from writing to individual branches within the repo using branch permissions.
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