Don't register cfgfile flags on flag.CommandLine in func init()

[blakerouse]

Proposed commit message

Requires the explicit calling of cfgfile.InitFlags(nil) to register the flags initialized by the cfgfile module.

This is required to allow other modules to import beats without having those flags present in the global flag.CommandLine. When they are automatically registered they collide and cause issues with other already registered command line arguments (aka. elastic-agent).

Checklist

• 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 change to the default configuration files
• [ ] I have added tests that prove my fix is effective or that my feature works (not really possible to unit test)
• [ ] I have added an entry in CHANGELOG.next.asciidoc or CHANGELOG-developer.next.asciidoc. (not user facing)

Disruptive User Impact

None

[elasticmachine]

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

[mergify]

This pull request does not have a backport label.
If this is a bug or security fix, could you label this PR @blakerouse? 🙏.
For such, you'll need to label your PR with:

• The upcoming major version of the Elastic Stack
• The upcoming minor version of the Elastic Stack (if you're not pushing a breaking change)

To fixup this pull request, you need to add the backport labels for the needed
branches, such as:

• backport-8./d is the label to automatically backport to the 8./d branch. /d is the digit

[mergify]

backport-8.x has been added to help with the transition to the new branch 8.x.
If you don't need it please use backport-skip label and remove the backport-8.x label.