Fix/shadow env in container (#646)

* fix: shadow .env file in container to prevent agents from reading secrets

The main agent's container mounts the project root read-only, which
inadvertently exposed the .env file containing API keys. Mount /dev/null
over /workspace/project/.env to shadow it — secrets are already passed
via stdin and never need to be read from disk inside the container.

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

* fix: adapt .env shadowing and runtime for Apple Container

Apple Container (VirtioFS) only supports directory mounts, not file
mounts. The previous /dev/null host-side mount over .env crashes with
VZErrorDomain "A directory sharing device configuration is invalid".

- Dockerfile: entrypoint now shadows .env via mount --bind inside the
  container, then drops privileges via setpriv to the host UID/GID
- container-runner: main containers skip --user and pass RUN_UID/RUN_GID
  env vars so entrypoint starts as root for mount --bind
- container-runtime: switch to Apple Container CLI (container), fix
  cleanupOrphans to use container list --format json
- Skill: add Dockerfile and container-runner.ts to
  convert-to-apple-container skill (v1.1.0)

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

* fix: revert src to Docker runtime, keep Apple Container in skill only

The source files should remain Docker-compatible. The Apple Container
adaptations live in the convert-to-apple-container skill and are applied
on demand.

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

---------

Co-authored-by: Claude Opus 4.6 <noreply@anthropic.com>

.claude/skills/convert-to-apple-container/modify/container/Dockerfile.intent.md

@@ -0,0 +1,31 @@
+# Intent: container/Dockerfile modifications
+
+## What changed
+Updated the entrypoint script to shadow `.env` inside the container and drop privileges at runtime, replacing the Docker-style host-side file mount approach.
+
+## Why
+Apple Container (VirtioFS) only supports directory mounts, not file mounts. The Docker approach of mounting `/dev/null` over `.env` from the host causes `VZErrorDomain Code=2 "A directory sharing device configuration is invalid"`. The fix moves the shadowing into the entrypoint using `mount --bind` (which works inside the Linux VM).
+
+## Key sections
+
+### Entrypoint script
+- Added: `mount --bind /dev/null /workspace/project/.env` when running as root and `.env` exists
+- Added: Privilege drop via `setpriv --reuid=$RUN_UID --regid=$RUN_GID --clear-groups` for main-group containers
+- Added: `chown` of `/tmp/input.json` and `/tmp/dist` to target user before dropping privileges
+- Removed: `USER node` directive — main containers start as root to perform the bind mount, then drop privileges in the entrypoint. Non-main containers still get `--user` from the host.
+
+### Dual-path execution
+- Root path (main containers): shadow .env → compile → capture stdin → chown → setpriv drop → exec node
+- Non-root path (other containers): compile → capture stdin → exec node
+
+## Invariants
+- The entrypoint still reads JSON from stdin and runs the agent-runner
+- The compiled output goes to `/tmp/dist` (read-only after build)
+- `node_modules` is symlinked, not copied
+- Non-main containers are unaffected (they arrive as non-root via `--user`)
+
+## Must-keep
+- The `set -e` at the top
+- The stdin capture to `/tmp/input.json` (required because setpriv can't forward stdin piping)
+- The `chmod -R a-w /tmp/dist` (prevents agent from modifying its own runner)
+- The `chown -R node:node /workspace` in the build step