refactor: rename skills to workflows

[xpcmdshell]

What

• Renames agent-facing concept and namespace from skills to workflows across the codebase.
• Updates file/redis storage wiring, subprocess/container bootstrap, MCP server tools, and docs/examples to use workflows.
• Fixes a few regressions introduced during the rename (kernel init string escaping, tool registry loading, tests with embedded newlines).

Why

• Align terminology + public API with the refactor (workflows are the persisted unit).
• Restore core functionality after the rename so Session, MCP, SubprocessExecutor, and ContainerExecutor all work end-to-end.

Validation

• Focused reruns of previously failing modules:
  • tests/test_mcp_server.py
  • tests/test_session.py (including -m slow)
  • tests/test_negative.py
  • tests/test_storage_vector_store.py
  • tests/test_vector_store.py
  • tests/test_redis_tools.py
  • tests/container/
• Rebuilt Docker images after container server changes:
  • docker/Dockerfile.base -> py-code-mode:base
  • docker/Dockerfile.tools -> py-code-mode-tools:latest

Notes

• Pyright still reports optional-dep typing noise in container/vector-store code paths (fastapi/docker/httpx/chromadb). This PR focuses on functional correctness and minimal typing boundary fixes where they affected core behavior.