refactor: replace message.Warn with context logger

[phillebaba]

Description

This change replaces use of message.Warn with structured logging.

Related Issue

Depends on #2842
Relates to #2576

Checklist before merging

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

[codecov]

Codecov Report

Attention: Patch coverage is 12.65823% with 207 lines in your changes missing coverage. Please review.

Files with missing lines	Patch %	Lines
src/pkg/logging/handler.go	0.00%	29 Missing ⚠️
src/pkg/packager/deploy.go	13.33%	13 Missing ⚠️
src/cmd/package.go	0.00%	12 Missing ⚠️
src/pkg/utils/wait.go	0.00%	11 Missing ⚠️
src/internal/packager/helm/post-render.go	0.00%	8 Missing ⚠️
src/pkg/cluster/data.go	0.00%	8 Missing ⚠️
src/cmd/dev.go	0.00%	7 Missing ⚠️
src/internal/agent/start.go	0.00%	7 Missing ⚠️
src/pkg/cluster/tunnel.go	0.00%	7 Missing ⚠️
src/pkg/packager/remove.go	0.00%	7 Missing ⚠️
... and 36 more

Files with missing lines	Coverage Δ
src/internal/agent/hooks/argocd-application.go	75.00% <ø> (-0.93%)	⬇️
src/internal/agent/hooks/argocd-repository.go	78.26% <ø> (-0.47%)	⬇️
src/internal/agent/hooks/flux-gitrepo.go	86.04% <ø> (-0.63%)	⬇️
src/internal/agent/hooks/flux-helmrepo.go	78.26% <100.00%> (-0.91%)	⬇️
src/internal/agent/hooks/flux-ocirepo.go	83.60% <100.00%> (-0.53%)	⬇️
src/internal/packager/images/push.go	0.00% <ø> (ø)
src/internal/packager/template/template.go	60.60% <100.00%> (ø)
src/pkg/layout/component.go	0.00% <ø> (ø)
src/pkg/layout/package.go	37.50% <ø> (+0.83%)	⬆️
src/pkg/message/message.go	10.23% <ø> (+0.46%)	⬆️
... and 47 more

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