refactor(skill/atomic-chat-tool): ship MCP file in skill folder, revert src edits

The initial /add-atomic-chat-tool merge added src edits directly to main.
That conflicts with the utility-skill pattern used elsewhere (e.g. /claw):
the skill folder should ship the file and SKILL.md should instruct copy +
idempotent edits at install time, not a git merge that carries src diffs.

- Move container/agent-runner/src/atomic-chat-mcp-stdio.ts →
  .claude/skills/add-atomic-chat-tool/atomic-chat-mcp-stdio.ts
- Revert the atomic_chat mcpServers entry in agent-runner index.ts
- Revert mcp__atomic_chat__* from TOOL_ALLOWLIST in providers/claude.ts
- Revert ATOMIC_CHAT_* env forwarding and [ATOMIC] log elevation in
  src/container-runner.ts
- Empty .env.example back out
- Rewrite SKILL.md: copy the shipped file, then apply deterministic Edits
  (index.ts, providers/claude.ts, container-runner.ts, .env.example)
  with exact before/after snippets the installer agent can match.

Main is now back to its pre-PR state for the tool; /add-atomic-chat-tool
re-applies everything at install time.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

.env.example

@@ -1,7 +0,0 @@
-# Atomic Chat MCP tool (skill/atomic-chat-tool)
-# Override the host where Atomic Chat exposes its OpenAI-compatible API.
-# Default: http://host.docker.internal:1337 (with fallback to localhost)
-# ATOMIC_CHAT_HOST=http://host.docker.internal:1337
-
-# Optional API key. Leave unset for a local Atomic Chat install — it does not require auth.
-# ATOMIC_CHAT_API_KEY=