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chore: migrate additional permissions to PermissionProfile (#12731)
This PR replaces the old `additional_permissions.fs_read/fs_write` shape with a shared `PermissionProfile` model and wires it through the command approval, sandboxing, protocol, and TUI layers. The schema is adopted from the `SkillManifestPermissions`, which is also refactored to use this unified struct. This helps us easily expose permission profiles in app server/core as a follow-up.
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@@ -8,8 +8,8 @@ When you need extra filesystem access for one command, use:
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- `sandbox_permissions: "with_additional_permissions"`
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- `additional_permissions` with one or both fields:
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- `fs_read`: list of paths that need read access
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- `fs_write`: list of paths that need write access
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- `file_system.read`: list of paths that need read access
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- `file_system.write`: list of paths that need write access
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This keeps execution inside the current sandbox policy, while adding only the requested permissions for that command, unless an exec-policy allow rule applies and authorizes running the command outside the sandbox.
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