enhancement: Refactor notes for the capabilities work

[nabil1440]

Blocker: no. Do not fix these items separately. Include them in the capability refactor.

Defect

• internal/utils contains unrelated code. internal/utils/version.go and internal/version have similar names but different functions.
• The commands are package-level *cobra.Command variables, and init() registers them. This makes tests difficult.
• The command logic and the output (color.*) are in the same functions.
• RunCompose connects directly to os.Stdin, os.Stdout and os.Stderr. Thus, other code cannot capture the output.
• The exec calls and the HTTP calls do not use context.Context. Thus, other code cannot cancel them.
• cmd/base.go and cmd/global.go contain the fixed path /home/fly. FindComposeFile uses $HOME. Thus, the configuration has two sources.
• --domain is a persistent root flag. base, sites, status and version accept it, but they ignore it.
• The root check compares cmd.Name() with "update".
• The code uses yaml.v2 only to get the service names. yaml.v2 gets no more updates.
• The directory checks in status belong in the monitoring capability.
• Small items:
  • startAllSites and stopAllSites contain the same code.
  • cmd/base.go:24-25 contains code that cannot run.
  • interface{} can be any.
  • cmd/root.go contains scaffold comments.
  • The CLI does not show CommitHash and BuildDate. Use rootCmd.Version.

Cost

• The control plane needs operations that return results and errors. The current structure does not supply them.
• An agent that operates for a long time needs cancellation and timeouts. The current calls do not have them.
• Two configuration sources can give different paths on the same server.
• The agent will operate as a service. The current root check does not support a privilege model for a service.

Benefit of the fix

• Each capability gets operations that it can test, cancel and connect to the control plane.
• One configuration source gives the same paths everywhere.
• docker compose config --services can replace yaml.v2. This command also reads override files and environment variables.