fix(config): ensured env vars take precedence over in-code config

[aryamohanan]

This is the first PR addressing configuration precedence.

The goal of this change is to ensure the correct order between environment variables and in-code configuration:

env > in-code

Currently, the precedence between these two sources is mixed. This PR corrects that behavior.

Added missing logging in the configuration file when a config is set.

Scope of This PR

This PR only fixes the precedence between:

• Environment variables
• In-code configuration

Agent configuration precedence will be addressed in separate follow-up PRs.

Future Work

Additional PRs will follow to correct the agent configuration order.

• Update order env> in-code fix(config): ensured env vars take precedence over in-code config #2409
• Add new method in core ->config->index to sync agent config
• Refactor code avoid use of activate fn config
• Integration tests
• More tests (manual + e2e)

Migration Plan

This change will be released in the next major version (v6), planned for Q2 2026.

ref https://jsw.ibm.com/browse/INSTA-80965

Epic : https://jsw.ibm.com/browse/INSTA-817

[sonarqubecloud]

Quality Gate passed

Issues
0 New issues
0 Accepted issues

Measures
0 Security Hotspots
93.3% Coverage on New Code
0.0% Duplication on New Code

See analysis details on SonarQube Cloud