docs: refresh README for tools added since last update

[sr320]

What changed

The README's Repository Structure section still described the repo as docs/ + protocols/ + equipment_manuals/ + lab_safety_docs/ + two config files. It was missing everything added over the past year. This brings it current.

Added — Data Catalogs and Web Tools

• docs/histology-explorer/ — the Histology Databank Explorer, plus a pointer to its build scripts and README
• data-portal/ — Nightingales sequencing libraries + reference genomes browser, and how build.py regenerates its JSON
• igv_server/ — IGV genome registry and annotation files

Added — Automation

• .github/workflows/ — Pages deploy on push to master, 15-minute server probe, Markdown URL checker
• .github/ISSUE_TEMPLATE/
• scripts/ — the status probers, with a one-line note on why there are two of them (raven is not in public DNS, so the in-network cron is the only thing that can see it)

Updated

• Expanded the docs/ bullet to cover sections that have grown since the last README pass: onboarding/offboarding, project management, writing and oral presentation guides, agentic coding tools, and the standalone HTML tutorials
• Quick Start now links Onboarding, Computing Hardware (with its live status lights), and the two data catalogs
• Issue reporting points at issues/new/choose — the old bare issues/new link bypassed the templates in .github/ISSUE_TEMPLATE/
• Noted that handbook-navigated protocols live in docs/protocols/, distinct from top-level protocols/

Notes for reviewers

• All four new handbook URLs were checked and return 200.
• Docs-only change; no code or config touched.
• Two things left alone deliberately: html/tjgr.markdown (one orphaned file) and the root-level UW_NWGC_Library_Submission_Form_2019.docx — neither was in the old README either.
• .readthedocs.yml is described factually rather than as removed. It's still present but pins Python 3.7 while the live site deploys via GitHub Actions, so it may be worth deleting in a separate change if Read the Docs is genuinely no longer in use.

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