fix: Application config takes precedence over Template

[sweb]

Description

The precedence rules described in the documentation were not followed wrt Application and ApplicationTemplate. Also notes special treatment of jvmArgumentOverrides.

This is in a way breaking, because more specific values were swallowed before - fixing this can impact what's actually now executed.

Definition of Done Checklist

• Not all of these items are applicable to all PRs, the author should update this template to only leave the boxes in that are relevant
• Please make sure all these things are done and tick the boxes

Author

• Changes are OpenShift compatible
• CRD changes approved
• CRD documentation for all fields, following the style guide.
• Helm chart can be installed and deployed operator works
• Integration tests passed (for non trivial changes)
• Changes need to be "offline" compatible
• Links to generated (nightly) docs added
• Release note snippet added

Reviewer

• Code contains useful comments
• Code contains useful logging statements
• (Integration-)Test cases added
• Documentation added or updated. Follows the style guide.
• Changelog updated
• Cargo.toml only contains references to git tags (not specific commits or branches)

Acceptance

• Feature Tracker has been updated
• Proper release label has been added
• Links to generated (nightly) docs added
• Release note snippet added
• Add type/deprecation label & add to the deprecation schedule
• Add type/experimental label & add to the experimental features tracker

[razvan]

thanks. the cli args are never used but the jvm prop fix is good.