[{"type":"thinking","thinking":"The user says: most important note — DO NOT WRITE to any research documents. Only touch website-related files. Put this in the plan. And earlier they answered \"Plan + build now\".\n\nSo now: write RH-WEBSITE.md (repo root — is that a research document? No, it's a website plan file; NGUYEN.md, STATE.md, research/* are research documents. RH-WEBSITE.md is website-related, at repo root as discussed). Then build the website in web/.\n\nThis is a big task. Let me set up a todo list and get going. Also save a memory about this directive (feedback memory: never write to research documents; website work only touches web/ + RH-WEBSITE.md).\n\nPlan of implementation:\n\n1. Write RH-WEBSITE.md (plan doc with the DO-NOT-WRITE rule prominent).\n2. Install Django + markdown into .venv (pip install). Check pip availability. Django on Python 3.14 — Django 5.2+ supports 3.14? Django 5.2 supports Python 3.10–3.13 officially; Django 6.0 supports 3.12-3.14? Actually Django 6.0 (Dec 2025) supports Python 3.12, 3.13, 3.14. Should be fine. Let me just pip install django and see.\n3. Create project structure:\n   - web/manage.py\n   - web/rhweb/ (settings, urls, wsgi)\n   - web/dashboard/ (views, urls, templates, static)\n   - web/feedback/ + feedback.db (created at runtime)\n   - web/logs/\n4. Templates: base.html with left sidebar, pages: home, dashboard, roadmap, ledger, experiments (+ detail w/ Plotly), derivations, graveyard, journal, resources, paper, live runs, feedback (submit + search).\n5. API: /api/status/ polling endpoint, /api/logtail/, /api/health/.\n6. Parsers: STATE.md sections, NGUYEN.md checklist, research.db queries, JSON sidecars, markdown rendering.\n7. Start server detached, verify.\n\nThe user said plan + build now. This is a lot of work but let's go. Keep code reasonably concise but complete. Use vanilla JS + Plotly vendored. Plotly vendored — I need to download plotly.min.js (~3.5MB). Internet may be available (pip install). I can pip download or fetch from CDN. Alternatively use CDN link with local fallback? User said localhost only, but their machine has internet presumably. Vendored is safer. I can download plotly via pip (plotly python package includes plotly.js in plotly/package_data? Actually plotly.js is in plotlywidget or in plotly/offline). `pip install plotly` then copy plotly/package_data/plotly.min.js. That works offline.\n\nKaTeX: could vendor from katex npm — harder. Alternative: MathJax via CDN, or skip math rendering? Markdown files contain LaTeX. Simplest robust: use MathJax 3 CDN... but no CDN dependency desired. KaTeX dist can be downloaded via pip? There's `katex` on npm not pip. Could download from jsdelivr with curl. Let me try curl to fetch katex dist files. If network works for pip, curl to CDN likely works too.\n\nSimpler: write a small download step in the build; if it fails, fall back to CDN link. Given time, maybe just use CDN links for KaTeX/MathJax with a note, and vendor Plotly from pip package. Actually for localhost-only with internet available, CDN is acceptable... but user emphasized robustness. Compromise: vendor Plotly from pip; use MathJax CDN? Hmm.\n\nActually, let me check: pip download for plotly gets us plotly.min.js inside the wheel. For KaTeX, I can curl from https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/katex.min.js and katex.min.css + fonts. Fonts are many files; the CSS references fonts folder. Downloading all fonts is annoying. Alternative: MathJax 3 single-file tex-chtml.js (~1MB?) also references no external fonts (uses its own bundled). MathJax tex-chtml.js is self-contained (~1.5MB). Vendor that: curl https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-chtml.js. That's one file, self-contained. \n\nLet me plan the build steps:\n\n1. TodoWrite task list.\n2. Save memory (feedback: never write research docs; website project context).\n3. Write RH-WEBSITE.md.\n4. pip install django markdown plotly (plotly just for vendored js; or curl plotly.min.js directly — one file: https://cdn.plot.ly/plotly-2.35.2.min.js ~3.7MB). curl both files.\n5. Scaffold Django project manually (write files directly rather than django-admin startproject, more control).\n6. Implement views/parsers/templates/static.\n7. Run migrations (feedback uses SQLite via Django model in web/feedback.db? Simpler: use Django's default db.sqlite3 inside web/ for feedback model + also write JSON files. Requirement: folder with file or database. I'll do both: Django model in web/feedback.db (configure DATABASES to point there) + JSON file per submission in web/feedback/.\n8. Start server detached, health check, verify pages via curl.\n9. Commit? NGUYEN.md session protocol says git commit at session end — but this is a separate project; user said don't touch research docs. Git commit of web/ + RH-WEBSITE.md — should I commit? The repo's protocol commits everything. Adding new files is not \"writing to research documents\". I'll ask or just commit at end? The user said \"Plan + build now\" — I'll build, test, and commit web/ + RH-WEBSITE.md with a clear message (website files only). Actually committing is an action visible... it's local git, reversible. The session protocol mandates commits. But this isn't a research session per se. I'll commit at the end and mention it; or ask. I'll just do it — local commit, standard practice here, only website files staged by name.\n\nLet me think about the Django implementation in more detail to keep it manageable:\n\nsettings.py: DEBUG=True, ALLOWED_HOSTS=['127.0.0.1','localhost'], ROOT = Path(__file__).resolve().parent.parent.parent (repo root). RESEARCH_DIR = ROOT/'research'. DATABASES: default → web/feedback.db.\n\nModels: Feedback(id auto, created, name, category, text, status, notes). Migration needed — run makemigrations + migrate.\n\nViews:\n- home: static content + summary stats (counts from db).\n- dashboard: parse STATE.md (CURRENT POSITION, NEXT ACTION, BLOCKERS sections), progress metrics: parse NGUYEN.md checklist counting [x]/[~]/[ ] tasks; ledger count from results table; recent git log (subprocess git log --oneline -10); new feedback count.\n- roadmap: NGUYEN.md §5 rendered as markdown (just render whole NGUYEN.md? It's the blueprint — render it). Simpler: roadmap page renders NGUYEN.md markdown.\n- ledger: query results table + render R files.\n- experiments: list from experiments table joined with JSON sidecars; detail page /experiments/E-015/ renders sidecar + charts. Charts: generic — read CSV via pandas? Avoid pandas dependency in web (it's in venv already though — pandas is in research stack? requirements lists pandas; check installed. Even so, csv module suffices). Chart spec: for selected experiments, define chart configs (x col, y col(s)) in a dict; generic chart view loads CSV (limit rows, maybe downsample) and emits JSON to template, Plotly renders.\n- derivations/graveyard/journal/resources: markdown file listings + rendered view pages.\n- paper: render draft.tex? LaTeX rendering is hard; show status + link to PDFs list + bib entries count. Simple page with paper folder info.\n- liveruns: list *-run.log files with mtime/size; tail endpoint returns last N lines; JS polls every 3s.\n- feedback: form (name optional, category select, text) → save JSON + DB; search page with q + filters.\n\nAPI:\n- /api/health/ → {\"ok\": true}\n- /api/status/ → {state_mtime, state: {next_action, position}, nguyen_mtime, db_mtime, running_logs: [{file, mtime, size}], new_feedback: n, latest_experiment...}\n- /api/logtail/?file=E-021-run.log&n=200 → safe: only files matching *-run.log in data dir.\n\nMarkdown rendering: python-markdown with extensions (tables, fenced_code). MathJax handles $...$ in rendered HTML — need to prevent markdown from mangling math (underscores). Use pymdownx? Simpler: markdown with 'mdx_math'? python-markdown doesn't handle math natively; underscores inside math get italicized. Option: use markdown2? Also mangles. Common trick: protect math spans before markdown conversion (regex extract $...$ and $$...$$, replace with placeholders, restore after). I'll implement that — ~20 lines.\n\nTemplates: base.html with sidebar menu, top status bar (current task + live indicator). Pages extend base. CSS: single static css file, dark theme, clean.\n\nJS: status polling script (updates dashboard panels + sidebar badge), logtail poller, Plotly chart loader, MathJax config.\n\nFile count ~25 files. Manageable. Let me be efficient: write files with Write tool.\n\nDirectory layout:\n\nweb/\n├── manage.py\n├── requirements-web.txt\n├── rhweb/\n│   ├── __init__.py\n│   ├── settings.py\n│   ├── urls.py\n│   └── wsgi.py\n├── dashboard/\n│   ├── __init__.py\n│   ├── apps.py\n│   ├── models.py        (Feedback)\n│   ├── views.py\n│   ├── api.py           (or in views)\n│   ├── urls.py\n│   ├── research_data.py (parsers: state, checklist, db, sidecars, markdown)\n│   ├── migrations/__init__.py\n│   ├── templates/dashboard/\n│   │   ├── base.html\n│   │   ├── home.html\n│   │   ├── dashboard.html\n│   │   ├── roadmap.html\n│   │   ├── ledger.html\n│   │   ├── experiments.html\n│   │   ├── experiment_detail.html\n│   │   ├── markdown_page.html  (generic for derivations/journal/resources/graveyard/paper)\n│   │   ├── live_runs.html\n│   │   └── feedback.html\n│   └── static/dashboard/\n│       ├── style.css\n│       ├── app.js\n│       └── vendor/plotly.min.js, tex-chtml.js\n├── feedback/            (JSON files, created at runtime)\n├── logs/                (server.log)\n└── feedback.db          (runtime)\n\nKeep views in one views.py + research_data.py. \n\nCharts config: define in research_data.py CHARTS = {\"E-015\": {...}, \"E-023\": ..., \"E-002\": ...}. For experiment detail, if config exists, render chart. Also generic table preview (first 50 rows).\n\nDownsampling: E-002 zeros CSV has 10⁴ rows — fine for Plotly scatter. E-023 margin 20k rows — downsample to ~2000.\n\nLet me now check what's installed in .venv (django presence) and pip install. Start executing.\n\nTodos:\n1. Write RH-WEBSITE.md plan (with DO-NOT-WRITE rule)\n2. Install web deps (Django, markdown) + vendor JS assets\n3. Scaffold Django project (web/)\n4. Implement data parsers (research_data.py)\n5. Implement views + API endpoints\n6. Templates + CSS + JS\n7. Migrate DB, start server detached, verify pages\n8. Commit website files\n\nLet me start. First todo list, memory save, then go.\n\nFor pip: ./.venv/Scripts/python.exe -m pip install django markdown. Python 3.14 — Django version: latest (6.0.x?) supports 3.14? Django 5.2 LTS (April 2025) supports Python 3.10-3.13. Django 6.0 (Dec 2025) supports 3.12-3.14. pip will resolve an appropriate version. Fine.\n\nVendor JS: curl -L https://cdn.plot.ly/plotly-2.35.2.min.js and https://cdn.jsdelivr.net/npm/mathjax@3.2.2/es5/tex-chtml.js. If curl fails, note fallback.\n\nGit bash on Windows has curl usually. OK.\n\nNow STATE.md parsing: sections are \"## CURRENT POSITION\", \"## NEXT ACTION\" (line after heading), \"## BLOCKERS\". I'll parse headings generically.\n\nNGUYEN.md checklist parsing: lines starting with \"- [x]\"/\"- [~]\"/\"- [ ]\" within §5. Count.\n\nresearch.db access: sqlite3 directly (read-only URI mode to avoid locks: sqlite3.connect(f\"file:{path}?mode=ro\", uri=True)).\n\nJSON sidecars: read from numerics/data.\n\nMarkdown protect-math approach.\n\nSecurity: localhost only, DEBUG True fine. Feedback form: CSRF token, sanitization via Django templates (autoescape). Search uses parameterized queries via ORM. Log tail: whitelist regex ^[\\w-]+-run\\.log$ and resolve within data dir.\n\nLet me write everything now. I need to be careful about length but complete. Start.","signature":""},{"type":"text","text":"Understood — hard rule noted: **website work touches only `web/` and `RH-WEBSITE.md`; the research archive is read-only for this project.** I'll put it at the top of the plan. Starting now."},{"type":"tool_use","id":"TodoWrite_12","name":"TodoWrite","input":{"todos":[{"content":"Write RH-WEBSITE.md plan (with DO-NOT-WRITE rule at top)","status":"in_progress","activeForm":"Writing RH-WEBSITE.md plan"},{"content":"Install web deps (Django, markdown) + vendor Plotly/MathJax JS","status":"pending","activeForm":"Installing web dependencies"},{"content":"Scaffold Django project in web/","status":"pending","activeForm":"Scaffolding Django project"},{"content":"Implement research data parsers (read-only)","status":"pending","activeForm":"Implementing data parsers"},{"content":"Implement views + API endpoints + feedback system","status":"pending","activeForm":"Implementing views and API"},{"content":"Build templates, CSS, JS (sidebar layout, charts, live polling)","status":"pending","activeForm":"Building templates and assets"},{"content":"Migrate DB, start server detached, verify pages","status":"pending","activeForm":"Starting and verifying server"},{"content":"Commit website files (web/ + RH-WEBSITE.md only)","status":"pending","activeForm":"Committing website files"}]},"extra_content":null}]