chore: unexport cmd functions besides NewZarfCommand

[AustinAbro321]

Description

This will unexport all commands besides NewZarfCommand. This keeps the surface area of breaking changes small, while giving users a while to directly embed Zarf with Cobra.

This flattens the src/cmd package as well which enables unexporting functions, and makes the structure simpler all around. We no longer need a separate common package to avoid import cycles.

Related Issue

Fixes #2765 (Technically the issue could have already been closed, it's more intentional this time though)

Checklist before merging

• Test, docs, adr added or updated as needed
• Contributor Guide Steps followed

[netlify]

✅ Deploy Preview for zarf-docs canceled.

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[codecov]

Codecov Report

Attention: Patch coverage is 0% with 388 lines in your changes missing coverage. Please review.

Files with missing lines	Patch %	Lines
src/cmd/package.go	0.00%	97 Missing ⚠️
src/cmd/dev.go	0.00%	63 Missing ⚠️
src/cmd/internal.go	0.00%	42 Missing ⚠️
src/cmd/zarf_tools.go	0.00%	37 Missing ⚠️
src/cmd/tools.go	0.00%	33 Missing ⚠️
src/cmd/initialize.go	0.00%	31 Missing ⚠️
src/cmd/root.go	0.00%	24 Missing ⚠️
src/cmd/crane.go	0.00%	16 Missing ⚠️
src/cmd/archiver.go	0.00%	12 Missing ⚠️
src/cmd/connect.go	0.00%	9 Missing ⚠️
... and 11 more

Files with missing lines	Coverage Δ
src/cmd/helm/dependency.go	0.00% <ø> (ø)
src/cmd/helm/dependency_build.go	0.00% <ø> (ø)
src/cmd/helm/dependency_update.go	0.00% <ø> (ø)
src/cmd/helm/flags.go	0.00% <ø> (ø)
src/cmd/helm/load_plugins.go	0.00% <ø> (ø)
src/cmd/helm/repo.go	0.00% <ø> (ø)
src/cmd/helm/repo_add.go	0.00% <ø> (ø)
src/cmd/helm/repo_index.go	0.00% <ø> (ø)
src/cmd/helm/repo_list.go	0.00% <ø> (ø)
src/cmd/helm/repo_remove.go	0.00% <ø> (ø)
... and 24 more

[soltysh]

lgtm