fix(cli): hide the repl scaffold from --help, answer repl --help instead of hijacking the terminal

[plombeer31]

What

atomic-agent --help advertised repl Interactive debug REPL: step the agent manually — but the command is an M1 scaffold whose only working inputs are help
and quit. Worse, repl --help did not answer the help request: it opened the
readline prompt, swallowed the terminal, and answered unknown command: --help.

Two small changes:

1. Hidden from the top-level help. CommandDescriptor gains a hidden flag;
   printHelp filters on it. The command still dispatches when typed — nothing
   breaks for anyone who uses it — it is just no longer advertised as a feature.
2. repl --help / -h answers before readline starts. Prints a short usage
   note that states the scaffold status and exits 0, instead of dropping into the
   interactive prompt.

Testing

• 2 new unit tests. The discriminator is built in: under vitest, stdin is a pipe
  that never closes, so on the unpatched code both tests hang in the readline loop
  until the 15 s timeout (verified: 2/2 fail on main, 2/2 pass with the patch).
• e2e against the built CLI: --help no longer lists repl (the only remaining
  match is the word "replace" in the config summary); repl --help prints the
  note and exits 0 immediately.
• npm run lint (tsc) clean.