fix(smolmachines): mount git-gate files at boot via virtiofs staging dirs

Two issues caused krun_start_enter -22 (VM boot crash):

1. git-gate entrypoint missing at boot: sidecar_init.py starts all
   daemons (including git-gate) immediately as PID 1. The entrypoint
   was copied in via machine_cp which only runs after machine_start
   returns — too late. virtiofs also can't mount files at root (/).

   Fix: bake a static /git-gate-entrypoint.sh wrapper into the
   Dockerfile.sidecars image that delegates to /etc/git-gate/entrypoint.sh.
   For smolmachines, stage per-bottle scripts with correct in-VM names
   under the git-gate state dir and virtiofs-mount to /etc/git-gate/ at
   VM creation time. docker/macOS backends are unchanged (their file
   bind-mount/docker cp still overrides the static wrapper).

2. Egress confdir mounted read-only: egress_entrypoint.sh writes
   combined-trust.pem to confdir under set -e; mitmproxy also needs
   to write its per-host cert cache there. Both fail fatally on a
   read-only virtiofs mount.

   Fix: change the egress confdir virtiofs mount to writable.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

bot_bottle/backend/smolmachines/launch.py

@@ -14,6 +14,7 @@ from __future__ import annotations
 
 import dataclasses
 import os
+import shutil
 from contextlib import ExitStack, contextmanager
 from pathlib import Path
 from typing import Callable, Generator
@@ -32,12 +33,7 @@ from ..docker.egress import (
     EGRESS_PORT as _EGRESS_PORT,
     egress_tls_init,
 )
-from ..docker.git_gate import (
-    GIT_GATE_ACCESS_HOOK_IN_CONTAINER,
-    GIT_GATE_CREDS_DIR_IN_CONTAINER,
-    GIT_GATE_ENTRYPOINT_IN_CONTAINER,
-    GIT_GATE_HOOK_IN_CONTAINER,
-)
+from ..docker.git_gate import GIT_GATE_CREDS_DIR_IN_CONTAINER
 from ...git_gate import (
     provision_git_gate_dynamic_keys,
     revoke_git_gate_provisioned_keys,
@@ -61,6 +57,14 @@ from .local_registry import crane_push_tarball, ephemeral_registry
 _REPO_DIR = str(Path(__file__).resolve().parent.parent.parent.parent)
 
 
+# In-VM directory containing git-gate scripts staged for virtiofs mount.
+# The Dockerfile.sidecars static wrapper at /git-gate-entrypoint.sh
+# delegates to this path, so the smolmachines backend can supply the
+# per-bottle entrypoint via a directory virtiofs mount instead of a
+# post-boot machine_cp (which runs too late for PID 1 daemons).
+_GIT_GATE_SCRIPTS_DIR_IN_VM = "/etc/git-gate"
+
+
 # Per-host cache for `smolvm pack create` outputs. Keyed by the
 # docker image ID so a Dockerfile change automatically invalidates
 # the cache. `pack create` is idempotent on the smolvm side but
@@ -358,6 +362,47 @@ def _port_for_label(label: str) -> int:
     raise ValueError(f"unknown sidecar forward label: {label}")
 
 
+def _stage_git_gate_for_smolvm(
+    plan: SmolmachinesBottlePlan,
+) -> tuple[Path, Path]:
+    """Stage git-gate scripts and credentials as virtiofs-mountable dirs.
+
+    virtiofs requires directory sources; the per-bottle git-gate scripts
+    have host-side names that differ from their in-VM paths (e.g.
+    `git_gate_entrypoint.sh` → `entrypoint.sh` in /etc/git-gate/), so
+    they cannot be expressed as parent-dir mounts without renaming.
+
+    Copies them into per-bottle staging dirs under the git-gate state
+    dir. Returns `(scripts_dir, creds_dir)`:
+      - scripts_dir is mounted to /etc/git-gate/ in the sidecar VM;
+        the image's static /git-gate-entrypoint.sh wrapper delegates there.
+      - creds_dir is mounted to /git-gate/creds/ in the sidecar VM."""
+    gp = plan.git_gate_plan
+    state_dir = git_gate_state_dir(plan.slug)
+
+    scripts_dir = state_dir / "smolvm-scripts"
+    scripts_dir.mkdir(parents=True, exist_ok=True)
+    shutil.copy2(str(gp.entrypoint_script), str(scripts_dir / "entrypoint.sh"))
+    shutil.copy2(str(gp.hook_script), str(scripts_dir / "pre-receive"))
+    shutil.copy2(str(gp.access_hook_script), str(scripts_dir / "access-hook"))
+    for name in ("entrypoint.sh", "pre-receive", "access-hook"):
+        (scripts_dir / name).chmod(0o755)
+
+    creds_dir = state_dir / "smolvm-creds"
+    creds_dir.mkdir(parents=True, exist_ok=True)
+    for u in gp.upstreams:
+        keypath = Path(expand_tilde(u.identity_file))
+        dest_key = creds_dir / f"{u.name}-key"
+        shutil.copy2(str(keypath), str(dest_key))
+        dest_key.chmod(0o600)
+        if u.known_hosts_file:
+            dest_kh = creds_dir / f"{u.name}-known_hosts"
+            shutil.copy2(str(u.known_hosts_file), str(dest_kh))
+            dest_kh.chmod(0o600)
+
+    return scripts_dir, creds_dir
+
+
 def _bundle_launch_spec(
     plan: SmolmachinesBottlePlan, network: str, proxy_host: str,
 ) -> _bundle.BundleLaunchSpec:
@@ -378,33 +423,32 @@ def _bundle_launch_spec(
 
     # --- egress -----------------------------------------------
     ep = plan.egress_plan
-    volumes.append((str(ep.mitmproxy_ca_host_path), EGRESS_CA_IN_CONTAINER, True))
+    # virtiofs (smolvm) requires directory mounts — mount the CA's
+    # parent dir so mitmproxy-ca.pem lands at the right in-VM path.
+    # Writable so egress_entrypoint.sh can write combined-trust.pem
+    # and mitmproxy can create its per-host cert cache.
+    volumes.append((
+        str(ep.mitmproxy_ca_host_path.parent),
+        str(Path(EGRESS_CA_IN_CONTAINER).parent),
+        False,
+    ))
     if ep.routes:
         volumes.append((str(ep.routes_path.parent), str(Path(EGRESS_ROUTES_IN_CONTAINER).parent), True))
     env.extend(egress_sidecar_env_entries(ep))
 
     # --- git-gate ---------------------------------------------
+    # virtiofs requires directory mounts; git-gate scripts have
+    # host-side names that differ from their in-VM paths. Stage
+    # them with correct names under the git-gate state dir and
+    # mount those staging dirs. The image's static wrapper at
+    # /git-gate-entrypoint.sh delegates to the staged entrypoint,
+    # so the per-bottle script is available at VM boot time.
     gp = plan.git_gate_plan
     if gp.upstreams:
         daemons += ["git-gate", "git-http"]
-        volumes += [
-            (str(gp.entrypoint_script), GIT_GATE_ENTRYPOINT_IN_CONTAINER, True),
-            (str(gp.hook_script), GIT_GATE_HOOK_IN_CONTAINER, True),
-            (str(gp.access_hook_script), GIT_GATE_ACCESS_HOOK_IN_CONTAINER, True),
-        ]
-        for u in gp.upstreams:
-            keypath = expand_tilde(u.identity_file)
-            volumes.append((
-                keypath,
-                f"{GIT_GATE_CREDS_DIR_IN_CONTAINER}/{u.name}-key",
-                True,
-            ))
-            if u.known_hosts_file:
-                volumes.append((
-                    str(u.known_hosts_file),
-                    f"{GIT_GATE_CREDS_DIR_IN_CONTAINER}/{u.name}-known_hosts",
-                    True,
-                ))
+        scripts_dir, creds_dir = _stage_git_gate_for_smolvm(plan)
+        volumes.append((str(scripts_dir), _GIT_GATE_SCRIPTS_DIR_IN_VM, True))
+        volumes.append((str(creds_dir), GIT_GATE_CREDS_DIR_IN_CONTAINER, True))
 
     # --- supervise --------------------------------------------
     sp = plan.supervise_plan
@@ -415,7 +459,13 @@ def _bundle_launch_spec(
             f"SUPERVISE_DB_PATH={DB_PATH_IN_CONTAINER}",
             f"SUPERVISE_PORT={SUPERVISE_PORT}",
         ]
-        volumes.append((str(sp.db_path), DB_PATH_IN_CONTAINER, False))
+        # virtiofs requires directory mount — mount the DB's parent
+        # dir so bot-bottle.db lands at the right in-VM path.
+        volumes.append((
+            str(sp.db_path.parent),
+            str(Path(DB_PATH_IN_CONTAINER).parent),
+            False,
+        ))
 
     # Container ports the agent reaches from the smolvm guest —
     # published on `proxy_host` so the TSI allowlist and the docker