docs: name bot-bottle, not ./cli.py, in every instruction

`doctor` told users to run `./cli.py backend setup`. cli.py is a four-line
wrapper at the repo root that calls bot_bottle.cli:main, and it does not ship —
[tool.setuptools.packages.find] includes only bot_bottle*, so anyone who
installed rather than cloned has no such file. Confirmed against a real
install: the user's tree contains exactly one executable, `bot-bottle`, and no
cli.py anywhere, while doctor recommended `./cli.py` three times. Invisible in
development, where ./cli.py works fine from a checkout, which is why only a
clean-install test surfaced it.

The two entry points are the same code, so the fix is to name the one that
always exists. 141 replacements across 45 files: the runtime messages that
caused this, plus README, docs, PRDs, research notes and test prose, so nothing
teaches the invocation a user cannot run.

scripts/demo.sh is deliberately untouched — it *executes* ./cli.py from a
checkout, where that is the correct and available path.

Verified end to end: a sandbox install now reports
"Run: bot-bottle backend setup --backend=firecracker", and bot-bottle is on
that user's PATH. Unit suite unchanged against the pre-existing baseline.

Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01WEfZZhakx13bxTfXcZCoS5

docs/prds/0060-commit-bottle-state.md

@@ -30,12 +30,12 @@ snapshot before a planned host reboot or hardware migration.
 
 ## Goals / Success Criteria
 
-- `./cli.py commit [<slug>]` takes a snapshot of the running agent and
+- `bot-bottle commit [<slug>]` takes a snapshot of the running agent and
   stores it as a local artifact.
 - Without a slug argument the command shows the same interactive picker
   as `start` (the list of active slugs).
 - The committed artifact reference is stored in per-bottle state so
-  that the next `./cli.py resume <slug>` automatically uses the
+  that the next `bot-bottle resume <slug>` automatically uses the
   snapshot instead of rebuilding from the Dockerfile.
 - `mark_preserved` is called so the state dir survives the normal
   session-end cleanup.
@@ -81,7 +81,7 @@ to the committed `.smolmachine` artifact.
 ### `commit` command
 
 ```
-./cli.py commit [<slug>]
+bot-bottle commit [<slug>]
 ```
 
 1. Resolve slug (arg or interactive picker from `enumerate_active_agents`).