Add offline mode for air-gapped Docker deployments

[scampion]

Summary

• Add --offline CLI flag to run with pre-cached dependencies (no network access at runtime)
• Configure pyodide to use local packages from node_modules instead of CDN
• Update Dockerfile to pre-cache all dependencies during build (npm + pyodide packages)

Why offline mode?

Many enterprise and research environments operate in air-gapped networks where containers cannot access external registries or CDNs at runtime. This is
common in:

• Secure/classified environments with strict network isolation policies
• Edge deployments with limited or no internet connectivity
• Regulated industries (finance, healthcare, government) requiring reproducible, auditable builds
• CI/CD pipelines that enforce network-disabled test environments

This feature allows the Docker image to be fully self-contained — all dependencies (npm packages and pyodide Python packages) are cached during build,
enabling the MCP server to run without any network access.

Changes

• mcp_run_python/_cli.py: Add --offline argument
• mcp_run_python/main.py: Support offline mode - copy node_modules, skip install step, pass --cached-only to deno
• mcp_run_python/deno/src/runCode.ts: Set pyodide indexURL to local node_modules/pyodide/
• Dockerfile: Run deno install + noop mode during build to pre-cache packages; default to --offline in entrypoint
• smoke_test.sh: Add basic smoke test script

Test plan

• Build Docker image: docker build -t mcp-run-python .
• Run container without network: docker run --network none -p 3001:3001 mcp-run-python
• Verify with smoke test: ./smoke_test.sh