fix: sync stdout buffer to file

[daanschipper]

Description

The trivy command is completed and as it is the main process the entire container is stopped before the stdout buffer is cleared, resulting in malformed output.

This patch has been running for over a month and I have not experienced any lingering scan vulnerability jobs which could not be removed by the operator anymore. Used kube_job_complete{namespace="trivy-system", condition="true", job_name=~"scan-vulnerabilityreport-[0-9a-f]+"} to alert for scan jobs with malformed output.

I did refactor the getCommandAndArgs function to deduplicate the logic for compressed and not compressed mode, it was essentially the same. Also ensured the options are in alphabetic order.

Related issues

• Close Unexpected EOF log and vulnerability report no data #1792.

Checklist

• I've read the guidelines for contributing to this repository.
• I've added tests that prove my fix is effective or that my feature works.
• I've updated the documentation with the relevant information (if needed). Not applicable.
• I've added usage information (if the PR introduces new options). Not applicable.
• I've included a "before" and "after" example to the description (if the PR is a user interface change). Not applicable.

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[daanschipper]

Also updated the *-expected-scan.yaml files for the envtest.

[daanschipper]

@chen-keinan could you trigger the workflow again? 🙏

[daanschipper]

I'm running the failing integration test tests/e2e/config/fs-sbom.yaml locally on the latest origin/HEAD (18e40db), but the test is failing there as well. I'm observing the following

• The scan-vulnerabilityreport Job gets created
• The scan-vulnerabilityreport-xxxxxx Pod get created and completes successfully. The logs get outputted as expected
• The trivy operator outputs the following logs and does not create a VulnerabiltyReport

2024-08-26T11:49:25Z    DEBUG    reconciler.scan job    Pod must have been deleted    {"job-results-processor": "trivy-system/scan-vulnerabilityreport-9845bdc5f"}                                                                                                                                                      2024-08-26T11:49:25Z    DEBUG    reconciler.scan job    Deleting complete scan job    {"job": "trivy-system/scan-vulnerabilityreport-9845bdc5f", "owner": {"apiVersion": "v1", "kind": "Pod", "namespace": "e2e-test", "name": "my-pod"}}                                                                               2024-08-26T11:49:25Z    DEBUG    reconciler.scan job    Ignoring cached job that must have been deleted    {"job": "trivy-system/scan-vulnerabilityreport-9845bdc5f"} 

I'm not sure how to continue from here. The failing integration test seems to test pkg/plugins/trivy/filesystem.go which I did not edit.