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/research/malicious-commit-scanning.md

@@ -84,7 +84,7 @@ dangerous changes before they left*.
    (`supervise_gitleaks_allow`, [`git_gate_render.py`](../../bot_bottle/git_gate_render.py)).
    Extend the same flow to **high-risk file classes**: any commit touching
    CI/build/deploy scripts, auth/crypto code, egress config, or
-   adding/changing dependencies → route to `./cli.py supervise`. This is
+   adding/changing dependencies → route to `bot-bottle supervise`. This is
    attribution/policy, not detection, and it's the strongest thing here —
    a human on exactly the temporal-escape surfaces.
 4. **LLM semantic diff-review — the behavioral backstop.** The only
@@ -146,7 +146,7 @@ preserves the bottom-up distribution funnel.
   **governed code-egress review**, not "we resell inference" (the
   monetization notes explicitly warn against reselling compute).
 - **The web-console supervise/review flow — the strongest anchor.** Turn
-  the CLI `./cli.py supervise` approval into a real review surface:
+  the CLI `bot-bottle supervise` approval into a real review surface:
   rendered diff + finding context, approve/reject, **who-approved audit
   trail, RBAC on approvers, mobile/phone-control** (ties to the
   dashboard/vault north star). This is "central enforcement +