{
  "file_path": "D:\\Python\\Quantum\\research\\numerics\\scripts\\E-010-suzuki-W-function.py",
  "new_string": "    if theta in (0.0, np.pi):\n        def Wdirect(z):\n            V = hat_FT(np.array([z]), hh)[0] * float(\n                np.exp(1j * z * x) @ cp)\n            if theta == 0.0:\n                return 2 * (z * V.real + V.imag)\n            return 2 * (z * V.imag - V.real)\n        vals = Wf\n        idx = np.flatnonzero(np.sign(vals[:-1]) * np.sign(vals[1:]) < 0)\n        roots = []\n        for i in idx:\n            try:\n                roots.append(scipy.optimize.brentq(Wdirect, zg[i],\n                                                 zg[i + 1], xtol=1e-13,\n                                                 rtol=1e-13))\n            except ValueError:\n                pass",
  "old_string": "    if theta in (0.0, np.pi):\n        roots = find_zeros(lambda z: np.interp(z, zg, Wf), zg)\n        # refine by direct evaluation\n        def Wdirect(z):\n            V = hat_FT(np.array([z]), hh)[0] * float(\n                np.exp(1j * z * x) @ cp)\n            if theta == 0.0:\n                return 2 * (z * V.real + V.imag)\n            return 2 * (z * V.imag - V.real)\n        roots = [scipy.optimize.brentq(Wdirect, r - 0.02, r + 0.02)\n                 for r in roots]",
  "replace_all": false
}

{
  "filePath": "D:\\Python\\Quantum\\RH-WEBSITE.md",
  "oldString": "   header + row-number gutter, numeric right-align) + JSON sidecars.",
  "newString": "   header + row-number gutter, numeric right-align) + JSON sidecars +\n   collapsible verbatim source-code view.",
  "originalFile": "# RH-WEBSITE.md \u2014 NGUYEN-RH-1 Research Website\n# Standing plan + operations document. READ FIRST when doing website work.\n# Created: 2026-08-19 | Status: ACTIVE | Version: 1.0\n# ============================================================\n\n## 0. \u26d4 HARD RULE \u2014 READ FIRST (user directive, 2026-08-19)\n**DO NOT WRITE to any research document.** The research archive\n(NGUYEN.md, STATE.md, everything under `research/`, git history) is the\nsingle source of truth and is modified ONLY by the research agent per\nNGUYEN.md \u00a78.4. Website work may touch ONLY:\n- `D:\\Python\\Quantum\\web\\`          (all website code, data, logs)\n- `D:\\Python\\Quantum\\RH-WEBSITE.md` (this file)\n\nThe website reads research files exclusively through READ-ONLY handles:\nSQLite via `mode=ro` URI, text files opened `'r'`. Feedback submissions\ngo to `web/feedback/` + `web/feedback.db` \u2014 never into `research/`.\nWhen committing, stage ONLY `web/` and `RH-WEBSITE.md` by name.\n\n## 1. PURPOSE\nPublic-facing-style (localhost-only) interactive dashboard for the\nNGUYEN-RH-1 Riemann Hypothesis research project. Goals:\n- Landing page explaining RH and the research mission to a general audience.\n- Live progress: current stage, next action, metrics \u2014 auto-updating as the\n  research agent writes to the file system.\n- Browsable archive: results, experiments (+ interactive charts),\n  derivations, graveyard, journal, resources atlas, paper status.\n- Feedback channel: visitors submit comments/suggestions; searchable;\n  researcher reviews them to help the research.\n\n## 2. ARCHITECTURE\n- Location: `D:\\Python\\Quantum\\web\\` \u2014 Django project `rhweb`, app `dashboard`.\n- Interpreter: project `.venv` (`./.venv/Scripts/python.exe`).\n  Deps: `web/requirements-web.txt` (Django, markdown).\n- Server: `python web/manage.py runserver 127.0.0.1:8001` \u2014 localhost only.\n- Frontend: vanilla JS + vendored Plotly.js (interactive charts) +\n  vendored MathJax (tex-chtml) for math in markdown. NO CDN dependency.\n- Live updates: frontend polls `GET /api/status/` every 3 s; the endpoint\n  reports file mtimes + parsed STATE.md + active run-logs + new-feedback\n  count + summary_stats (checklist counters, phase table, collection\n  counts); changed panels refresh in place. No WebSockets/Redis.\n\n### Data flow (all read-only on research/)\n| Source | How read | Used by |\n|---|---|---|\n| STATE.md | parse `## SECTION` blocks ('r') | Dashboard, status bar |\n| NGUYEN.md | checklist \u00a75 `- [x]/[~]/[ ]` counts; \u00a77 ledger | Dashboard metrics, Roadmap |\n| research/research.db | sqlite3 `file:...?mode=ro` | Ledger, Experiments, Derivations, Graveyard, Journal indexes |\n| research/numerics/data/*.json | json.load ('r') | Experiment cards (checks, key values, caveats) |\n| research/numerics/data/*.csv | csv module, downsampled | Plotly charts, table previews |\n| research/**/*.md | python-markdown + math-protect | Archive pages |\n| research/numerics/data/*-run.log | tail (last N lines) | Live Runs page |\n| git log | `git log --oneline` subprocess (read-only) | Dashboard activity feed |\n\n## 3. FILE MAP\n```\nweb/\n\u251c\u2500\u2500 manage.py\n\u251c\u2500\u2500 lockcheck.py              # \u00a70 verification: proves the server never\n\u2502                             #   blocks writers (run: .venv python web/lockcheck.py)\n\u251c\u2500\u2500 requirements-web.txt\n\u251c\u2500\u2500 rhweb/                  # project: settings.py, urls.py, wsgi.py\n\u251c\u2500\u2500 dashboard/\n\u2502   \u251c\u2500\u2500 research_data.py    # ALL read-only parsers (single module to audit \u00a70)\n\u2502   \u251c\u2500\u2500 models.py           # Feedback model (lives in web/feedback.db ONLY)\n\u2502   \u251c\u2500\u2500 views.py            # pages\n\u2502   \u251c\u2500\u2500 api.py              # /api/health, /api/status, /api/logtail\n\u2502   \u251c\u2500\u2500 urls.py\n\u2502   \u251c\u2500\u2500 templates/dashboard/*.html\n\u2502   \u2514\u2500\u2500 static/dashboard/{style.css, app.js, vendor/plotly.min.js, vendor/tex-chtml.js}\n\u251c\u2500\u2500 feedback/               # one JSON per submission (dual storage)\n\u251c\u2500\u2500 feedback.db             # SQLite index for search (Django default DB)\n\u2514\u2500\u2500 logs/                   # server.log, healthcheck.log\n```\n\n## 4. PAGES (left sidebar)\n1. **Home** `/` \u2014 RH explainer, mission, 4 attack tracks, success ladder.\n2. **Dashboard** `/dashboard/` \u2014 current stage (STATE.md), next action,\n   progress metrics (phases bar, tasks done/total, ledger size), git feed.\n3. **Roadmap** `/roadmap/` \u2014 NGUYEN.md \u00a75 checklist rendered w/ status.\n4. **Search** `/search/` \u2014 global archive search (see \u00a77 note): AND-of-terms\n   case-insensitive scan across all MD_COLLECTIONS markdown; snippets with\n   line numbers + highlighted matches; results hits link to /ledger/R-NNN/.\n5. **Results Ledger** `/ledger/` + `/ledger/R-NNN/` \u2014 claims + honesty tags.\n6. **Experiments** `/experiments/` + `/experiments/E-NNN/` \u2014 sidecar cards;\n   Plotly charts from CSVs (config in research_data.CHARTS); pass/fail badges.\n7. **Scripts & Data** `/scripts/` + `/scripts/<stem>/` \u2014 all experiment\n   scripts; per-script data files (experiment-table links \u222a exact-stem\n   matches) shown as paginated spreadsheet tables (500 rows/page, sticky\n   header + row-number gutter, numeric right-align) + JSON sidecars.\n8. **Derivations** `/derivations/` + detail \u2014 37 D-files, math rendered.\n9. **Graveyard** `/graveyard/` \u2014 documented dead ends.\n10. **Journal** `/journal/` + detail \u2014 session narratives.\n11. **Resources** `/resources/` + detail \u2014 43-note RH-equivalence atlas.\n12. **Paper** `/paper/` \u2014 draft status, references, paper-folder inventory.\n13. **Live Runs** `/live/` \u2014 tail view of *-run.log, 3 s polling.\n14. **Feedback** `/feedback/` \u2014 submit form + search (text, category, status).\n15. **Conversations** `/conversations/` \u2014 browse the Nguyen CLI conversation\n    index (`~/.nguyen/projects/D--Python-Quantum/agent.db`, outside the repo,\n    opened read-only): session list; per-session message cards with\n    thinking/tool blocks (collapsible), FTS search + kind filters; single\n    message view `/conversations/<spk>/msg/<id>/` with prev/next arrows,\n    arrow-key navigation, jump-to-id, raw JSON row view.\n\n## 5. FEEDBACK SYSTEM\n- Submit: name (optional), category (general/suggestion/question/correction/\n  track-A/B/C/D), text. CSRF-protected; autoescaped on render.\n- Dual storage (mirrors NGUYEN.md \u00a78.2): JSON file per submission in\n  `web/feedback/FB-<utc>-<id>.json` + row in `web/feedback.db`.\n- Search: full-text (name+text) + category/status filters.\n- Statuses: new \u2192 reviewed \u2192 acted-on (status changes are website data,\n  allowed under \u00a70; researcher notes field for follow-up).\n\n## 6. OPERATIONS\n### 6.1 Session-start protocol (website work)\n1. Read this file.\n2. Run `./.venv/Scripts/python.exe web/healthcheck.py --restart`\n   (checks /api/health + all routes + status-API freshness; restarts the\n   server if unreachable). Fix any failing route before other work.\n3. Check the watchdog is alive: `web/logs/watchdog.log` tail should show\n   entries within the last ~10 min; if not, restart it (\u00a76.2b).\n4. Review new feedback: `web/feedback.db` status='new' (or the /feedback/\n   page); surface relevant items to the user.\n5. Improvement pass (standing order, user 2026-08-19): look for at least\n   one interface or data-presentation improvement per session; log ideas\n   in \u00a78 below and implement the worthwhile ones.\n### 6.2 Start server (detached, sandbox DISABLED \u2014 long-run rule)\n```\ncd D:\\Python\\Quantum && ./.venv/Scripts/python.exe web/manage.py runserver \\\n  127.0.0.1:8001 >> web/logs/server.log 2>&1   # DETACHED_PROCESS\n```\n### 6.2b Watchdog (always-on monitoring, started 2026-08-19)\n`web/watchdog.py` runs detached between sessions: every 300 s it runs the\nhealth checks and restarts the server if unreachable. Logs:\n`web/logs/watchdog.log` + `web/logs/healthcheck.log`.\nStart detached: `subprocess.Popen([sys.executable, 'web/watchdog.py'], ...)`\nwith DETACHED_PROCESS (same pattern as \u00a76.2).\n### 6.3 Restart / health\n- Stop: find PID via `netstat -ano | findstr :8001`, `taskkill /PID <pid> /F`.\n- **Restart required after ANY code OR template change** (templates are\n  cached in-process \u2014 a home.html edit did not appear until restart,\n  2026-08-19). Static CSS/JS changes serve immediately.\n  NOTE: port is **8001** since 2026-08-19 \u2014 port 8000 is reserved for the\n  user's other service (do not use it).\n- Log tail: `web/logs/server.log`.\n- First run after code change to models:\n  `./.venv/Scripts/python.exe web/manage.py migrate`.\n### 6.4 Updating the site when research data changes shape\n- New experiment: automatic (db + sidecars). Charts: add entry to\n  `research_data.CHARTS` (x/y columns, type).\n- New markdown folders: register in `research_data.MD_COLLECTIONS`.\n- Never patch around \u00a70 \u2014 if a feature needs research-archive writes,\n  STOP and ask the user.\n### 6.5 Lock-safety guarantees (verified 2026-08-19, web/lockcheck.py)\n- Text/md/CSV/log reads use Python 'r' handles (Windows share mode allows\n  concurrent writers) and close immediately after each read.\n- research.db / agent.db opened SQLite mode=ro per query, closed in finally;\n  shared read lock exists only for the duration of each SELECT (ms).\n- Server runs --noreload: no autoreload file watchers held open.\n- git log is read-only plumbing (no index lock).\n- Empirical: 24 s of 4-thread HTTP load across all heavy pages while taking\n  120 DB write locks (BEGIN IMMEDIATE/ROLLBACK) + 360 write-intent file\n  opens on STATE.md, NGUYEN.md, CSVs, run-logs \u2014 zero conflicts, zero stalls.\n\n## 7. IMPROVEMENT BACKLOG (standing order \u2014 review each session)\nIdeas not yet implemented, ranked by value:\n1. Conversations: \"new activity\" badge when agent.db grows between polls.\n2. Experiments: diff view when a sidecar's checks change between runs.\n3. Charts: E-019 zero-flow needs series-column grouping support.\nDone:\n- 2026-08-27: Scripts & Data page `/scripts/` (user request) \u2014 index of all\n  45 research/numerics/scripts/*.py with their experiment links + data\n  files; detail pages render each CSV as a spreadsheet table (500-row\n  server-side pagination, sticky header, sticky row-number gutter with\n  true CSV line numbers, numeric-column right-align, hover stripes) and\n  each JSON sidecar as a collapsible pretty-printed block. Script\u2192data\n  mapping = experiments-table links \u222a exact-stem matches (verified: all\n  45 scripts resolve correctly; utility scripts show \"none registered\").\n  Routes added to healthcheck (now 24); traversal guard verified 404.\n- 2026-08-27: mobile/responsive sidebar (backlog #3) \u2014 at \u2264 900px the\n  sidebar goes off-canvas (translateX transition) behind a hamburger\n  button in the sticky topbar; backdrop tap, Escape, or any menu-link\n  click closes it; state is body.nav-open (aria-expanded wired);\n  content padding shrinks to 16px. Desktop layout unchanged.\n- 2026-08-27: dashboard + home stat counters auto-refresh (backlog #4) \u2014\n  /api/status/ now carries summary_stats(); app.js updates all counters\n  (dashboard: done/partial/open/results/experiments/feedback; home: done/\n  results/experiments/derivations/graveyard/sessions) every 3 s, and\n  rebuilds the dashboard phases table on change only (signature compare,\n  DOM-API build \u2014 no innerHTML). Static git-feed / recent-sessions tables\n  intentionally left server-rendered.\n- 2026-08-27: global search page `/search/` (backlog #1) \u2014 AND-of-terms\n  case-insensitive scan-on-query across all MD_COLLECTIONS markdown\n  (results/derivations/graveyard/journal/resources); up to 3 snippets per\n  file with line numbers + <mark> highlights; results hits mapped to\n  /ledger/R-NNN/; 100-file cap with truncation notice; sidebar entry;\n  /search/ + a sample query added to the healthcheck ROUTES (now 22).\n  Also: watchdog found dead (last log 2026-08-21) and respawned detached.\n- 2026-08-19: healthcheck.py + watchdog.py (\u00a76.1/\u00a76.2b); Home latest-result\n  card now dynamic (was hardcoded R-004); dashboard data-freshness line\n  (STATE.md/research.db/agent.db, live via polling); E-017 chart.\n- 2026-08-22: bug fixes. (1) git_log 500 on /dashboard/ \u2014 subprocess\n  decoded git's UTF-8 commit output as cp1252; reader thread died on\n  Unicode commit messages and stdout came back None. Fixed with\n  encoding=\"utf-8\", errors=\"replace\" + a None guard. (2) Roadmap Phase 2 /\n  5B checklists rendered as paragraph text \u2014 those phases have a note\n  paragraph directly above the list (no blank line) and python-markdown\n  never lets a list interrupt a paragraph (sane_lists or not). Fixed with\n  research_data._restore_interrupted_lists: inserts the missing blank line\n  before a list that follows paragraph text (skips indented item\n  continuations so existing lists stay tight; skips fenced code). Archive\n  text rendered verbatim as before \u2014 block structure only.\n- 2026-08-20: math typography pass APPLIED then REVERTED same day (user\n  directive). Context: MathJax 3.2.2 works (resources atlas has real\n  LaTeX); the research archive writes plain Unicode math, so MathJax has\n  nothing to typeset there \u2014 that is the correct, intended rendering.\n  A display-formula-lifting heuristic (research_data._display_formulas +\n  .math-line styling) was built and then removed at user request:\n  **the website renders the research archive VERBATIM \u2014 no presentation\n  transforms, no conversions, no re-boxing of archive text.** Do not\n  re-attempt Unicode\u2192LaTeX conversion or formula-detection heuristics;\n  the archive's plain-Unicode math is the source of truth and its\n  verbatim display is correct by definition.\n\n## 8. BUILD STATUS\n- [x] Plan written (v1.0, 2026-08-19)\n- [x] Dependencies installed (Django 6.1, markdown 3.10.3); vendored JS\n      (plotly 2.35.2, MathJax 3.2.2 tex-chtml)\n- [x] Django scaffold (rhweb project + dashboard app)\n- [x] Parsers / views / API (research_data.py read-only layer)\n- [x] Templates / CSS / JS (12 pages, sidebar, 3 s polling, Plotly charts)\n- [x] Server verified live at 127.0.0.1:8001 \u2014 all 15 routes 200;\n      feedback POST/search verified; path-traversal guard verified;\n      smoke-test data cleaned up\n- [x] Initial commit (web/ + RH-WEBSITE.md only)\n",
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        "+   collapsible verbatim source-code view.",
        " 8. **Derivations** `/derivations/` + detail \u2014 37 D-files, math rendered.",
        " 9. **Graveyard** `/graveyard/` \u2014 documented dead ends.",
        " 10. **Journal** `/journal/` + detail \u2014 session narratives."
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