docs: replace stale .sh paths with claude_bottle/*.py equivalents

Cleans up references to the pre-refactor bash layout (cli.sh,
lib/*.sh, scripts/*.sh) across README, Dockerfile, the pipelock PRD,
and research notes. Refreshes line numbers in the oauth-token note
against the current cli/start.py.

Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>

docs/research/oauth-token-exposure-to-claude.md

@@ -20,11 +20,12 @@ that does not route through `ANTHROPIC_BASE_URL` at all.
 
 ## How the token reaches claude today
 
-1. `cli.sh:526–528` — host's `CLAUDE_BOTTLE_OAUTH_TOKEN` is exported into
-   the launcher process as `CLAUDE_CODE_OAUTH_TOKEN`, then forwarded with
+1. `claude_bottle/cli/start.py` (around line 237–238) — host's
+   `CLAUDE_BOTTLE_OAUTH_TOKEN` is exported into the launcher process as
+   `CLAUDE_CODE_OAUTH_TOKEN`, then forwarded with
    `docker run -e CLAUDE_CODE_OAUTH_TOKEN` (no `=value`, so the value
    never lands on argv — good).
-2. `cli.sh:603–605` — claude is launched via
+2. `claude_bottle/cli/start.py` (around line 318–325) — claude is launched via
    `docker exec -it <container> claude …`, which inherits the container
    PID 1's env, including the token.
 3. claude runs as `node` (UID 1000) with `--dangerously-skip-permissions`.