chore: Upgrade crossplane

[jcogilvie]

Description of your changes

This PR upgrades crossplane-runtime from v2.1.0-rc.0 to v2.1.0-rc.1 and addresses compatibility issues
introduced by upstream changes to namespace propagation in Crossplane.

Dependency Upgrades

• ⬆️ github.com/crossplane/crossplane-runtime/v2: v2.1.0-rc.0 → v2.1.0-rc.1
• ⬆️ github.com/crossplane/crossplane/v2: v2.0.2 → v2.1.0-rc.1 (required for compatibility)

Key Changes

1. New Workaround: removeNamespacesFromClusterScopedResources()

Crossplane PR #6812 fixed issue
#6782 by making the render command propagate
namespaces from XRs to all composed resources. However, it doesn't check whether resources are cluster-scoped,
causing validation errors.

This function:

• Queries the cluster for each composed resource's CRD to determine scope
• Removes namespaces from cluster-scoped resources
• Includes detailed documentation (diff_processor.go:615-638) on the upstream fix needed

2. Removed Obsolete Workaround: propagateNamespacesToManagedResources()

The old workaround addressed issue #6782 (render not propagating namespaces), which is now fixed upstream. We no
longer need it since PR #6812 fixed the original problem.

3. Upstream Fix Documentation

Added inline documentation explaining:

• Root cause: SetComposedResourceMetadata() in Crossplane's render.go:455-457 blindly propagates
  namespaces without checking scope
• Proposed solution: Pass XRDs to render and check crd.Spec.Scope before setting namespaces
• Architectural constraint: render is an offline tool with no cluster access, so needs XRDs passed
  explicitly
• Migration path: Once upstream is fixed, we can remove our cleanup function

Testing

• ✅ All 31 integration tests pass
• ✅ All unit tests pass
• ✅ Verified namespace handling for both namespaced and cluster-scoped resources

Notes for Reviewers

• This is primarily a Renovate PR with compatibility fixes
• The workaround is clearly marked as temporary
• The code includes a detailed roadmap for the upstream fix needed in Crossplane

Fixes #

I have:

• Read and followed Crossplane's contribution process.
• Run earthly +reviewable to ensure this PR is ready for review.
• Added or updated unit tests.
• Added or updated e2e tests.
  - [ ] Linked a PR or a docs tracking issue to document this change.
  - [ ] Followed the API promotion workflow if this PR introduces, removes, or promotes an API.

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