BENCH-9860: Add a Nextflow Workbench development app

[samhornstein]

Add a Workbench Jupyter development app that hosts the Nextflow head process and gives a user's preferred agent access to the official Workbench MCP server. The app includes Nextflow 26.04.6, Java 17, lsof, a Nextflow skill, and the canonical Workbench startup hooks. A persistent home volume keeps the editable example and local Nextflow cache across container restarts.

The guide covers Git-based app creation, stdio MCP configuration, validation, and session-lock diagnosis. This app does not supervise Nextflow or reattach an orchestrator to in-flight Batch jobs; that is the separate BENCH-9854 request.

Validation

• JSON, Docker Compose configuration, skill validation, documentation links, and whitespace checks passed on this standalone branch.
• The pinned upstream MCP source compiled and answered stdio initialization/tool discovery (108 tools; no cloud calls).
• Docker image build and Workbench app creation, authentication, startup, and restart checks remain pending. The guide contains the test steps.

Jira: BENCH-9860