Refactor CLI code

[daniel-weisse]

Proposed changes

• Remove deprecated gramine-prepare command
• Move CLI code to cli/internal/cmd/
• Move Coordinator REST interaction to separate package
• Move helm interaction to separate package
• Move Kubernetes client setup to separate package
  • Could be further refactored by only returning a limited interface instead of a fully fledged Kubernetes client, but I think its fine for now
• Add package for file interaction

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[m1ghtym0]

Massive PR:O
Conceptually, the changes make sense to me.
I went over the changes but didn't do a throughout review of the code.
As most changes are refactoring I believe that the unit tests should ensure things are consistent.

[thomasten]

I got one question in certificate_test.go. Otherwise only nits. Choose yourself which ones you want to apply.