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>

container/agent-runner/src/index.ts

@@ -79,14 +79,6 @@ async function main(): Promise<void> {
       args: ['run', mcpServerPath],
       env: {},
     },
-    atomic_chat: {
-      command: 'bun',
-      args: ['run', path.join(__dirname, 'atomic-chat-mcp-stdio.ts')],
-      env: {
-        ...(process.env.ATOMIC_CHAT_HOST ? { ATOMIC_CHAT_HOST: process.env.ATOMIC_CHAT_HOST } : {}),
-        ...(process.env.ATOMIC_CHAT_API_KEY ? { ATOMIC_CHAT_API_KEY: process.env.ATOMIC_CHAT_API_KEY } : {}),
-      },
-    },
   };
 
   for (const [name, serverConfig] of Object.entries(config.mcpServers)) {