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/src/container-runner.ts.intent.md

@@ -0,0 +1,33 @@
+# Intent: src/container-runner.ts modifications
+
+## What changed
+Updated `buildContainerArgs` to support Apple Container's .env shadowing mechanism. The function now accepts an `isMain` parameter and uses it to decide how container user identity is configured.
+
+## Why
+Apple Container (VirtioFS) only supports directory mounts, not file mounts. The previous approach of mounting `/dev/null` over `.env` from the host causes a `VZErrorDomain` crash. Instead, main-group containers now start as root so the entrypoint can `mount --bind /dev/null` over `.env` inside the Linux VM, then drop to the host user via `setpriv`.
+
+## Key sections
+
+### buildContainerArgs (signature change)
+- Added: `isMain: boolean` parameter
+- Main containers: passes `RUN_UID`/`RUN_GID` env vars instead of `--user`, so the container starts as root
+- Non-main containers: unchanged, still uses `--user` flag
+
+### buildVolumeMounts
+- Removed: the `/dev/null` → `/workspace/project/.env` shadow mount (was in the committed `37228a9` fix)
+- The .env shadowing is now handled inside the container entrypoint instead
+
+### runContainerAgent (call site)
+- Changed: `buildContainerArgs(mounts, containerName)` → `buildContainerArgs(mounts, containerName, input.isMain)`
+
+## Invariants
+- All exported interfaces unchanged: `ContainerInput`, `ContainerOutput`, `runContainerAgent`, `writeTasksSnapshot`, `writeGroupsSnapshot`, `AvailableGroup`
+- Non-main containers behave identically (still get `--user` flag)
+- Mount list for non-main containers is unchanged
+- Secrets still passed via stdin, never mounted as files
+- Output parsing (streaming + legacy) unchanged
+
+## Must-keep
+- The `isMain` parameter on `buildContainerArgs` (consumed by `runContainerAgent`)
+- The `RUN_UID`/`RUN_GID` env vars for main containers (consumed by entrypoint.sh)
+- The `--user` flag for non-main containers (file permission compatibility)