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/prds/0001-per-agent-egress-proxy-via-pipelock.md

@@ -43,12 +43,12 @@ The feature works when all of the following are observable:
 
 The feature is **done** when all of the following ship:
 
-- `cli.sh start` brings up a per-agent pipelock sidecar on a `--internal`
+- `cli.py start` brings up a per-agent pipelock sidecar on a `--internal`
   Docker network and points the agent's `HTTPS_PROXY` at it.
 - A per-agent pipelock YAML config is generated from a bottle-level
   `egress.allowlist` field, plus baked-in defaults for Claude Code's
   required hosts so basic bottles work out of the box.
-- The existing `cli.sh` y/N preflight shows the resolved allowlist before
+- The existing `cli.py` y/N preflight shows the resolved allowlist before
   launch.
 - When the agent container exits, the pipelock sidecar and the internal
   network are torn down cleanly (no orphaned containers or networks).
@@ -76,7 +76,7 @@ The feature is **done** when all of the following ship:
 - Pipelock sidecar container lifecycle (start, attach to network,
   receive config, stop on agent exit).
 - `HTTPS_PROXY` / `HTTP_PROXY` injection into the agent container.
-- Preflight integration: the existing y/N plan in `cli.sh` lists the
+- Preflight integration: the existing y/N plan in `cli.py` lists the
   resolved allowlist.
 
 ### Out of scope
@@ -95,30 +95,31 @@ The feature is **done** when all of the following ship:
 
 ### New services / components
 
-Two new files under `lib/`:
+Two new modules under `claude_bottle/`:
 
-- **`lib/pipelock.sh`** — pipelock-specific logic. Generates the
-  per-bottle YAML config from the manifest's `egress` block plus baked-in
-  defaults; copies the YAML into the sidecar via `docker cp`; starts and
-  stops the sidecar container; resolves the allowlist for display in the
-  preflight.
-- **`lib/network.sh`** — Docker network plumbing. Creates the per-agent
-  `--internal` network (named `claude-bottle-net-<slug>` with the same
-  slug-and-suffix scheme used for container names), attaches the agent
-  and sidecar to it, removes it on teardown. Kept separate from
-  `lib/docker.sh` so a future PRD can add non-pipelock network controls
-  without entangling them with pipelock specifics.
+- **`claude_bottle/pipelock.py`** — pipelock-specific logic. Generates
+  the per-bottle YAML config from the manifest's `egress` block plus
+  baked-in defaults; copies the YAML into the sidecar via `docker cp`;
+  starts and stops the sidecar container; resolves the allowlist for
+  display in the preflight.
+- **`claude_bottle/network.py`** — Docker network plumbing. Creates the
+  per-agent `--internal` network (named `claude-bottle-net-<slug>` with
+  the same slug-and-suffix scheme used for container names), attaches
+  the agent and sidecar to it, removes it on teardown. Kept separate
+  from `claude_bottle/docker.py` so a future PRD can add non-pipelock
+  network controls without entangling them with pipelock specifics.
 
-This split mirrors the existing per-concern lib/ pattern
-(`manifest.sh`, `env_resolve.sh`, `skills.sh`, `ssh.sh`).
+This split mirrors the existing per-concern module pattern
+(`manifest.py`, `env_resolve.py`, `skills.py`, `ssh.py`).
 
 ### Existing code touched
 
-- **`cli.sh`** — wire the new lifecycle into `start`: create the
-  internal network, launch the pipelock sidecar, then launch the agent
-  container with `HTTPS_PROXY` / `HTTP_PROXY` set to the sidecar's
-  service name. Add the resolved allowlist to the preflight y/N output.
-  Tear down sidecar + network in the existing exit trap.
+- **`claude_bottle/cli/start.py`** — wire the new lifecycle into the
+  `start` subcommand: create the internal network, launch the pipelock
+  sidecar, then launch the agent container with `HTTPS_PROXY` /
+  `HTTP_PROXY` set to the sidecar's service name. Add the resolved
+  allowlist to the preflight y/N output. Tear down sidecar + network in
+  the existing exit handler.
 - **`README.md`** — public-facing description should mention that
   agent containers route HTTP egress through pipelock by default, and
   document the new `egress.allowlist` bottle field.
@@ -128,9 +129,10 @@ This split mirrors the existing per-concern lib/ pattern
 the image. This keeps the image agnostic to whether a sidecar is in use
 (useful if a future bottle definition opts out of the proxy for testing).
 
-`lib/docker.sh` may grow one or two helpers if there is a clean place
-for shared primitives, but the network-specific helpers live in
-`lib/network.sh`. Decide during implementation; not a contract.
+`claude_bottle/docker.py` may grow one or two helpers if there is a
+clean place for shared primitives, but the network-specific helpers
+live in `claude_bottle/network.py`. Decide during implementation; not a
+contract.
 
 ### Data model changes
 
@@ -174,9 +176,9 @@ bottle share the same allowlist.
 
 - **Pipelock binary** is pulled from
   `ghcr.io/luckypipewrench/pipelock@sha256:<digest>`. The digest is
-  pinned in `lib/pipelock.sh` (or a sibling `.env`-shaped constants
-  file) and bumped deliberately, mirroring the claude-code version
-  pinning pattern in `Dockerfile`.
+  pinned in `claude_bottle/pipelock.py` (or a sibling constants module)
+  and bumped deliberately, mirroring the claude-code version pinning
+  pattern in `Dockerfile`.
 - No new host-side runtimes. The pipelock image is the only new
   external artifact.
 
@@ -189,10 +191,10 @@ bottle share the same allowlist.
   which features used by this PRD are Apache-2.0-core. v1's plan
   (proxy + 48 default DLP patterns + subdomain entropy + sidecar
   topology) is expected to be core-only, but this should be confirmed.
-- **Where to put the digest pin.** A constant in `lib/pipelock.sh` is
-  the lowest-friction option; a separate `lib/versions.sh` (or similar)
-  may be cleaner once there are multiple pinned dependencies. Decide
-  during implementation.
+- **Where to put the digest pin.** A constant in
+  `claude_bottle/pipelock.py` is the lowest-friction option; a separate
+  `claude_bottle/versions.py` (or similar) may be cleaner once there
+  are multiple pinned dependencies. Decide during implementation.
 - **Per-agent overrides.** The PRD scopes egress to the bottle. If a
   later use case calls for tightening (not loosening) the allowlist for
   one agent within a bottle, revisit. Out of scope for v1.

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**
 

docs/research/network-egress-guard.md

@@ -234,7 +234,7 @@ which does not work on macOS Desktop.
 
 Moderate. The script itself is well-understood and can be lifted nearly
 verbatim from Anthropic's devcontainer repo. The integration points in
-`cli.sh` are:
+`cli.py` are:
 
 1. Pass `--cap-add NET_ADMIN --cap-add NET_RAW` in the `docker run` invocation.
 2. `docker cp` an `init-firewall.sh` script into the container (alongside

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`.

docs/research/pipelock-assessment.md

@@ -273,7 +273,7 @@ reach, and avoids the `--best-effort` issue on macOS Docker Desktop.
 The claude-bottle manifest model would need one new piece of plumbing: a
 per-agent pipelock ACL YAML generated from the manifest's `allowlist`
 and `ssh` entries, analogous to what the smokescreen section of
-`network-egress-guard.md` already sketches. The `cli.sh` changes required
+`network-egress-guard.md` already sketches. The `cli.py` changes required
 are the same pattern: `docker network create --internal`, `docker run` for
 the proxy container, then `docker run` for the agent with `HTTPS_PROXY`
 injected.
@@ -408,7 +408,7 @@ The reasoning:
    subdomain-entropy DNS exfil detection, MCP scanning, and request
    redaction. The integration shape for claude-bottle is identical: a
    separate container on an internal Docker network, with the agent's
-   `HTTPS_PROXY` pointing at it. The `cli.sh` changes are the same pattern.
+   `HTTPS_PROXY` pointing at it. The `cli.py` changes are the same pattern.
 
 2. **The DLP layer is the most direct answer to the content-tripwire gap.**
    The `secret-exfil-tripwire-encodings.md` note concluded that no