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/host-dispatch-to-container-agents.md

@@ -34,7 +34,7 @@ Three pieces in combination give a 100% guarantee:
    - `get_status(job_id)` — check running/done
    - `get_output(job_id)` — read results
 
-3. **Non-interactive container run mode** — `cli.sh run <agent> "<task>"` passes the task to `claude --print` inside the container and captures output. Currently `cli.sh start` is interactive only; this mode does not yet exist.
+3. **Non-interactive container run mode** — `cli.py run <agent> "<task>"` passes the task to `claude --print` inside the container and captures output. Currently `cli.py start` is interactive only; this mode does not yet exist.
 
 ## Proposal
 
@@ -42,7 +42,7 @@ Build host-dispatch-to-container in two deliverables:
 
 **Deliverable 1: Non-interactive run mode for claude-bottle**
 
-Extend `cli.sh` with a `run <agent> <task>` subcommand. Starts the container, writes the task prompt to a file inside it (same `docker cp` pattern used for `--append-system-prompt-file`), invokes `claude --print` with the prompt, streams stdout back to the host, and exits when Claude finishes. Results committed and pushed from inside the container as usual.
+Extend `cli.py` with a `run <agent> <task>` subcommand. Starts the container, writes the task prompt to a file inside it (same `docker cp` pattern used for `--append-system-prompt-file`), invokes `claude --print` with the prompt, streams stdout back to the host, and exits when Claude finishes. Results committed and pushed from inside the container as usual.
 
 **Deliverable 2: MCP server wrapping claude-bottle**