[k8s] Fix System Integration to utilise hostfs mounts

[pkoutsovasilis]

What does this PR do?

This PR ensures that the Elastic Agent system integration correctly utilizes the /hostfs mount to collect host-level metrics. Previously, the system integration only monitored processes visible within the container due to missing configuration settings for the /hostfs path.

The changes include:

• Adding system.hostfs: /hostfs to all relevant system metricsets in both the Helm Chart templates and rendered manifests.

Why is it important?

Without this fix, the Elastic Agent system integration collects only container-level metrics instead of full host-level metrics. This leads to incomplete observability of the Kubernetes nodes and limits visibility into host performance and resource utilization.

By explicitly setting system.hostfs: /hostfs, the agent can correctly access host-level /proc and /sys files, ensuring comprehensive monitoring.

Checklist

• I have read and understood the pull request guidelines of this project.
• My code follows the style guidelines of this project.
• I have commented my code, particularly in hard-to-understand areas.
• I have made corresponding changes to the documentation.
• I have made corresponding changes to the default configuration files.
• I have added tests that prove my fix is effective or that my feature works.
• I have added an entry in ./changelog/fragments using the changelog tool.
• I have added an integration test or an E2E test.

Disruptive User Impact

This change does not introduce breaking changes, as it only enhances system integration behavior without modifying existing user configurations. However, users who previously relied on container-only monitoring should be aware that host-level metrics will now be collected.

How to test this PR locally

1. Deploy the Elastic Agent using the updated Helm Chart having system integration enabled.
2. Verify that /proc and /sys are mounted under /hostfs inside the container.
3. Validate that collected metrics reflect the host system rather than just the containerized environment.

Related issues

• Closes [k8s] System Integration Does Not Utilise /hostfs Mounts #6411

Questions to ask yourself

• How are we going to support this in production?
• How are we going to measure its adoption?
• How are we going to debug this?
• What are the metrics I should take care of?
• ...

[elasticmachine]

Pinging @elastic/elastic-agent-control-plane (Team:Elastic-Agent-Control-Plane)

[swiatekm]

This is also broken in https://github.com/elastic/elastic-agent/blob/main/deploy/kubernetes/elastic-agent-standalone-kubernetes.yaml, are we tracking that as a separate issue? Would probably be simplest to fix both at the same time.

[pierrehilbert]

Shouldn't we also backport this on 9.0 branch?

[elastic-sonarqube]

Quality Gate passed

Issues
0 New issues
0 Fixed issues
0 Accepted issues

Measures
0 Security Hotspots
No data about Coverage
No data about Duplication

See analysis details on SonarQube