refactor(cli): simplify command composition

[codyhartsook]

Summary

• Reduces cmd/kagent/main.go to a small entrypoint backed by a reusable root command
• Flattens and colocates command constructors under a consistent internal command structure
• Keeps root.go focused on composition while each command owns its Cobra wiring and flags
• Centralizes connection flags, session setup, and output handling
• Aligns CLI command composition with the agentregistry layout

The resulting boundary is intentionally small: Root() creates a fresh command tree, command packages own command-specific setup, and the shared connection package owns gRPC, TLS, and temporary port-forward setup. This removes package-level CLI flag state and keeps command behavior out of main.go.

tui-recording-pr.mp4

This is the third of three related CLI PRs and builds on #2559 and #2605. When reviewed as a stack, the changes unique to this PR are structural; the API v2 workflows and AgentInstance TUI behavior live in the first two PRs.

Related to #2366 and the K13 CLI cutover in docs/plans/api-v2-execution-plan.md.

Test plan

• make -C go test
• go test ./core/cli/...
• make -C go lint
• make -C go build
• API v2 E2E suite against a refreshed local Kind cluster
• CLI and AgentInstance TUI smoke tests against a local installation