bug: `project run --init-resources`/`--extra-resources` reject manifests with a leading comment document

[ytsarev]

What happened?

crossplane project run --init-resources <file> (and --extra-resources) fails with:

encountered an invalid or empty raw resource

whenever the manifest begins with a comment block before the first --- document separator — i.e. a file-level header comment, which is a very common convention. kubectl apply -f on the exact same file works, because it skips empty/null documents. So a manifest that is perfectly valid everywhere else in the ecosystem is rejected by project run.

How can we reproduce it?

cat > prereq.yaml <<'EOF'
# A header comment describing this file.
# It spans a few lines before the first resource.
---
apiVersion: v1
kind: Namespace
metadata:
  name: demo
EOF

# Fails:
crossplane project run --init-resources prereq.yaml
#   Error: encountered an invalid or empty raw resource

# The identical file applies fine with kubectl:
kubectl apply --dry-run=client -f prereq.yaml

Deleting the leading comment lines (so the file starts at the first resource), or moving the comment to after the first ---, makes the error go away. The same applies to --extra-resources.

Root cause

The YAML stream loader splits on --- and drops only byte-empty chunks, but a comment-only chunk is non-empty text, so it survives, unmarshals to an empty RawExtension, and ApplyResources then treats that empty resource as fatal:

1. cmd/crossplane/render/load.go — LoadYAMLStreamFromFile reads documents with k8s.io/apimachinery/pkg/util/yaml.NewYAMLReader and skips only chunks where len(bytes) == 0. The leading # ... block (before the first ---) is non-empty bytes, so it is returned as a document.

2. cmd/crossplane/project/run.go — each document is sigs.k8s.io/yaml.Unmarshal'd into a runtime.RawExtension. A comment-only document is valid YAML that unmarshals to null, leaving RawExtension.Raw empty (no error at this step).

3. internal/project/install.go — ApplyResources hard-fails on it:

   for _, raw := range resources {
       if len(raw.Raw) == 0 {
           return errors.New("encountered an invalid or empty raw resource")
       }
       ...

Suggested fix

Skip empty raw resources instead of erroring, matching how kubectl and the rest of the ecosystem treat empty/null documents. In ApplyResources:

if len(raw.Raw) == 0 {
    continue
}

That single spot covers both --init-resources and --extra-resources. Happy to open a PR with this plus a regression test if the approach looks right.

What environment did it happen in?

• Crossplane CLI version: v2.4.0 (also present on current main, 5342ad7 / v2.5.0-rc.0 — the ApplyResources code is unchanged)
• Platform: reproduced on darwin/arm64 and linux/amd64 (the logic is platform-independent)
• Crossplane version: n/a (fails client-side before contacting a control plane)