refactor(cli): group subcommand handlers under cli/commands/

Move the eleven per-command modules (backend, cleanup, commit, edit,
info, init, list, login, resume, start, supervise) into a new
bot_bottle/cli/commands/ package, leaving the dispatcher (__init__),
entrypoint (__main__), and shared helpers (_common, tui) at the cli
root. Makes the command surface obvious at a glance and separates
handlers from the plumbing that registers them.

Updated the dispatcher's COMMANDS imports to .commands.*, bumped the
moved files' relative-import depths (.._common, .. import tui, sibling
.start unchanged), and repointed test references to
bot_bottle.cli.commands.*. Full unit suite green (2243); CLI dispatch
verified via `python -m bot_bottle.cli --help`.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>

bot_bottle/cli/commands/cleanup.py

@@ -0,0 +1,67 @@
+"""cleanup: stop and remove all orphaned bot-bottle resources.
+
+Walks every registered backend (docker, firecracker, macos-container)
+so a single `./cli.py cleanup` reaps every backend's leftovers — a
+firecracker bottle's VM processes and run dirs won't survive a
+docker-only cleanup pass (issue addressed alongside #77).
+
+Each backend's `prepare_cleanup` enumerates its own resources;
+docker's `_list_orphan_state_dirs` consults
+`enumerate_active_agents()` for the union of live identities so
+state dirs of running non-docker bottles aren't reaped. State
+dirs are shared layout, so docker is the single owner of that
+bucket.
+
+State dirs with `.preserve` are intentionally never touched — they
+hold preserved sessions the operator may want to `resume`. Manual
+`rm -rf ~/.bot-bottle/state/<identity>` is the path for those.
+"""
+
+from __future__ import annotations
+
+import sys
+
+from ...backend import get_bottle_backend, has_backend, known_backend_names
+from ...log import info
+from .._common import read_tty_line
+
+
+def cmd_cleanup(_argv: list[str]) -> int:
+    # Order: stable backend iteration so the y/N output is
+    # deterministic across runs. Skip backends whose runtime
+    # isn't available on this host so e.g. macos-container
+    # doesn't error on Linux.
+    plans = [
+        (name, get_bottle_backend(name))
+        for name in known_backend_names()
+        if has_backend(name)
+    ]
+    prepared = [(name, b, b.prepare_cleanup()) for name, b in plans]
+
+    if all(p.empty for _, _, p in prepared):
+        info("no bot-bottle resources to clean up")
+        return 0
+
+    for name, _, plan in prepared:
+        if plan.empty:
+            continue
+        info(f"--- {name} backend ---")
+        plan.print()
+
+    if not _prompt_yes("remove all of the above?"):
+        info("cleanup: skipped")
+        return 0
+
+    for name, backend, plan in prepared:
+        if plan.empty:
+            continue
+        backend.cleanup(plan)
+    info("cleanup: done")
+    return 0
+
+
+def _prompt_yes(message: str) -> bool:
+    sys.stderr.write(f"bot-bottle: {message} [y/N] ")
+    sys.stderr.flush()
+    reply = read_tty_line()
+    return reply in ("y", "Y", "yes", "YES")