projects: Skip empty documents when applying init and extra resources

[ytsarev]

Description of your changes

crossplane project run --init-resources/--extra-resources rejected any manifest whose first YAML document is empty — most commonly a file-level comment header before the first ---, a very common convention — with:

encountered an invalid or empty raw resource

The YAML stream loader (LoadYAMLStreamFromFile) splits on --- and only drops byte-empty chunks, so a comment-only chunk survives, unmarshals to an empty runtime.RawExtension, and ApplyResources treated that as fatal. kubectl apply -f on the identical file works because it skips empty/null documents.

This changes ApplyResources to skip empty raw resources (matching kubectl) instead of erroring, which fixes both --init-resources and --extra-resources since they share the path. The existing EmptyRawErrors unit test becomes SkipsEmptyRaw, asserting an empty document is skipped and a real resource alongside it is still applied.

Encountered in modelplaneai/modelplane#365 , see run.sh there for additional context.

Reproduction

$ printf '# header comment\n---\napiVersion: v1\nkind: Namespace\nmetadata:\n  name: demo\n' > prereq.yaml

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

$ kubectl apply --dry-run=client -f prereq.yaml   # the same file applies fine

Fixes #207

I have:

• Read and followed Crossplane's contribution process.
• Run ./nix.sh flake check — passes locally (generate-check, go-lint, and test all green for this commit). Also verified go build ./..., go vet, gofmt, and golangci-lint run (0 issues) directly.
• Added or updated unit tests.
• Linked a PR or a docs tracking issue to document this change. Bug fix with no user-facing docs change.
• Added backport release-x.y labels to auto-backport this PR. Leaving the backport decision to maintainers.

[coderabbitai]

📝 Walkthrough

Walkthrough

Changes

Empty resource handling

Layer / File(s)	Summary
Skip empty resources and verify application internal/project/install.go, internal/project/install_test.go	ApplyResources skips empty RawExtension entries, while tests verify that a neighboring ConfigMap is still applied successfully.

Estimated code review effort: 1 (Trivial) | ~5 minutes

Suggested reviewers: jcogilvie

🚥 Pre-merge checks | ✅ 6

✅ Passed checks (6 passed)

Check name	Status	Explanation
Linked Issues check	✅ Passed	The changes satisfy #207 by skipping empty raw resources and preserving valid resources in the same manifest.
Out of Scope Changes check	✅ Passed	The diff stays focused on the bug fix and its test, with no obvious unrelated changes.
Breaking Changes	✅ Passed	Only internal/project files changed; no apis/** or cmd/** fields/flags were removed or renamed, and ApplyResources behavior was relaxed, not removed.
Feature Gate Requirement	✅ Passed	No apis/** changes or new experimental surface; the PR only skips empty raw resources in existing ApplyResources behavior.
Title check	✅ Passed	The title is descriptive, under the length limit, and matches the main change to skip empty documents during resource application.
Description check	✅ Passed	The description clearly explains the bug, the fix, and the updated test behavior, so it is related to the changeset.

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[coderabbitai]

Actionable comments posted: 1

🤖 Prompt for all review comments with AI agents

Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.

Inline comments:
In `@internal/project/install_test.go`:
- Around line 106-124: Convert the SkipsEmptyRaw test into the required
table-driven structure with args, want, and reason fields, covering the empty
raw extension alongside the real ConfigMap. Execute each case through the table
and compare returned errors using cmp.Diff with cmpopts.EquateErrors(), while
retaining assertions that the real resource is applied.

🪄 Autofix (Beta)

Fix all unresolved CodeRabbit comments on this PR:

• Push a commit to this branch (recommended)
• Create a new PR with the fixes

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ℹ️ Review info

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Run ID: 7db5d502-960b-4229-9610-fe7d182a755b

📥 Commits

Reviewing files that changed from the base of the PR and between 5342ad7 and e8cb075.

📒 Files selected for processing (2)

• internal/project/install.go
• internal/project/install_test.go