autophagous

A field manual for achieving autophagy through cyclic prolonged fasting — published as an Elm document with a cycle planner, a companion source index and a printable cycle log.

Not medical advice. The protocol carries contraindications, abort signals, an electrolyte warning, and a refeeding-syndrome section for a reason. The medical disclaimer ships in the footer of every content page and is a hard constraint of this repo, not decoration.

What's here

Five routes, all worn as the same house document (masthead → numbered sections → contents rail → disclaimer footer):

Route	Module	Contents
/	src/Page/Protocol.elm	The protocol broadsheet, Rev. 3 — 12 numbered sections: epistemic limits, the two switches (mTORC1/AMPK), safety, GLP-1, the cycle, priming, the fast, the five stages by the clock (0–96 h), the refeed, the rebuild, the cycle log, references
/plan	src/Page/Plan.elm	The cycle planner — enter the moment your last meal ends and the protocol's elapsed hours become dates: priming D−3 to D−1, hour 0, every stage crossing, the refeed windows, the rebuild weeks, the earliest next cycle. §02 is a live clock: hours elapsed, the stage you are standing in, the countdown to the next line, a needle on the 0–96 h ruler, and the abort signals in full. Exports the schedule as an .ics calendar. The plan rides in the URL (?start=&target=), so it is shareable and nothing is stored
/dosing	src/Page/Dosing.elm	The electrolyte sheet — §07's milligram targets converted into grams of salt, teaspoons, and the divided doses the protocol requires. Handles the trap that a "lite salt" is half table salt, so it takes twice the spoonfuls and brings sodium that has to come off the salt you were also going to add. A "what not to reach for" section costs out the things people use instead — Liquid I.V., sports drinks, coconut water, bone broth — with the §07 clause each one breaks
/resources	src/Page/Resources.elm	The source index — 19 citations, each routed to the best copy a reader can legally reach; DOI + access state, nothing rehosted. Every entry names the protocol sections that cite it
/legal	src/Page/Legal.elm	Terms and disclaimers — the long form of the footer warning: no medical advice, absolute exclusions, emergencies, assumption of risk, no warranty, liability, privacy, reuse

Plus one print artifact: typst/cycle-log.typ → /downloads/cycle-log.pdf, linked from §11 of the protocol.

Both themes ship. Light and dark follow the system preference, and a three-state control (System / Light / Dark) in the site nav overrides it, persisting to localStorage.

Quick start

mise install     # deno 2, elm 0.19.1, elm-test-rs, typst — pinned in mise.toml
deno install     # dependencies, from deno.json
deno task dev

There is no Node here, and no npm. Deno is the only JavaScript runtime — it runs Vite, wrangler, and the compiled Elm test bundle. Dependencies and tasks live in deno.json. A package.json survives, carrying one overrides block and nothing else — see Notes for contributors.

mise install is not optional. The Elm compiler and the test runner are not packages of any kind — deno task build and deno task test resolve the bare names elm and elm-test-rs off PATH, and mise.toml is the only place their versions are written down, including for CI. The first install compiles elm-test-rs from source (~40 s); see the note in mise.toml for why it comes from a fork.

Command	Does
deno task dev	Vite dev server
deno task build	Production build to dist/
deno task preview	Serve the built output
deno task test	elm-test-rs (routing, wall-clock conversion, the schedule, the calendar export)
deno task deploy	Build and push dist/ to Cloudflare Pages (skips the test gate — prefer pushing to main)
deno task print	Compile typst/cycle-log.typ → public/downloads/cycle-log.pdf — commit the PDF, the site links to it

Layout

src/
  boot.js            styles, then Elm; applies the stored theme pre-boot
  Main.elm           the TEA shell — all state, URL wiring, #anchor scrolling, theme
  Route.elm          pure routing + query params (no Cmd, no ports), unit-tested
  Doc.elm            the document format: masthead, rail, § numbering, clause marks, footer
  Citations.elm      the sources, once — manifest, addresses, and who cites what
  Cycle.elm          the cycle as data: stage boundaries + the schedule, in offsets
  Civil.elm          wall clock <-> Posix, the direction elm/time doesn't ship
  Clock.elm          where the reader is in the cycle right now — pure, from elapsed minutes
  Search.elm         the site index — hand-written, checked against the prose both ways
  Dose.elm           §07's requirements as arithmetic — mg of an element to g of salt
  Ruler.elm          the 0-96 h clock; plain on the protocol, needled on the planner
  Safety.elm         safety content two surfaces render — the same values, never a summary
  Ics.elm            the calendar export — a string on a data: URL, no port, no deps
  Page/*.elm         pure views, one per route
  theme.css          tokens only
  fonts.css          @font-face only (hand-maintained)
  protocol.css       components
public/
  404.html           keeps Pages' SPA fallback OFF — see docs/DEPLOY.md
  _headers           cache policy (immutable only where names are stable)
  _redirects         client routes — scoped, one line per route, no wildcard
  downloads/         compiled print artifacts (committed)
  fonts/             self-hosted woff2 + their OFL licence texts
typst/               print sources
docs/                the specs — see below

index.html has no mount node on purpose: Browser.application takes the whole <body>, and Route.title owns the document title once Elm boots.

Architecture rules

These are load-bearing. Breaking one is a bug, not a style difference.

• Doc numbers and frames; pages render. A page hands Doc.view one ordered section list; the contents rail and the § numbers both derive from that list, so they cannot disagree. Doc never learns what a stage card or a citation entry is. In-prose cross-references (see §09) are the one hand-maintained thing — reordering sections means grepping for §.
• Adding a route means adding a line to public/_redirects. Scoped redirects, no wildcard. The friction is deliberate.
• The cycle's numbers live in Cycle.elm, once. The stage boundaries (0/16/24/48/72/96 h) had been written three times over — the stage cards, the ruler's percentages, the planner. Three copies of one number is a number that will drift.
• No transitions, no animations, anywhere. The live clock re-renders once a minute; a value that changes is not motion (DESIGN-REQUIREMENTS §1). prefers-reduced-motion has nothing to reduce, and if that stops being true something was broken.
• No device detection; breakpoints in rem. A narrow window is a narrow layout, and a reader with a raised default font size reaches it sooner — which only a rem query delivers. Nothing may clip, and nothing hides behind a gesture: below 60rem — one narrow tier for all of the chrome — the site nav's routes move into a disclosure panel — absolutely positioned, so the bar's height never changes and the sticky rail below it keeps working off a token that cannot go stale. It does not slide, fade or dim (DESIGN-PRINCIPLES §2b).
• Search is in the rail, and results replace the sheet. The index is hand-written but checked against the rendered pages in both directions: a term must appear in the section it claims, an alias must not. The query lives in the model, not the URL — a plan is a document you keep, a search is a way of looking at one.
• Citations are one system. Citations.elm holds the sources; the protocol's §12 list and the source index both render Citations.line. The backlink table (sites) is hand-maintained but checked against the rendered protocol in both directions — a marker without a table entry fails, and so does a table entry with no marker.
• A derived surface may tighten, never loosen. The dosing sheet won't divide a day into fewer than three doses; §07 gives no number. That floor is the sheet's judgement and the page says so — adding your own number silently, or attributing it to the protocol, is the failure this names.
• A derived surface is not the protocol. The planner compresses only what has a time attached, links back to the section it compressed, and never paraphrases a contraindication — it links to it, at full strength (DESIGN-PRINCIPLES §3b). That holds for anything generated from it: every event in the exported calendar carries its protocol link too.
• The planner's plan lives in the URL, mirrored with replaceUrl — no storage, no port, and UrlChanged branches on the route changing rather than the URL changing so that echo doesn't reset the form (DESIGN-PRINCIPLES §3a).
• theme.css is tokens; protocol.css is components. Raw hex outside theme.css is a bug, and so is consuming a primitive where a role token exists.
• Safety content is never cut, collapsed, or softened — contraindications, abort signals, the potassium warning, refeeding syndrome, the disclaimer footer (DESIGN-REQUIREMENTS §5).
• The live site is not the print surface. Printables are typst-generated and never forced through the site's CSS (DESIGN-PRINCIPLES §print). The @media print rules are an emergency fallback carrying no design obligation.
• Self-hosted assets only. No CDNs. The two webfonts (Archivo Expanded 700 for display, JetBrains Mono 400/700 for data) are committed under public/fonts/ with their OFL licences. Body type stays a system serif on purpose — see DESIGN-REQUIREMENTS §3. Never set font-stretch or font-weight: 800 on the display voice; only one 700 cut ships.

The source index

src/Citations.elm is the single source of truth for citation metadata and access state. Link-first: nothing is rehosted. Every entry carries a CrossRef-verified DOI (17 of 19 — the Nobel citation and the ASA guidance aren't journal articles and have none) plus an Access state from Unpaywall, so a reader can see before clicking whether they'll hit free full text or a paywall. 14 of 19 are free to reach.

The local PDF archive this replaced was retired 2026-08-16 for two reasons: being free to read on PMC is not permission to rehost — only 3 of 19 are under an open licence — and a frozen PDF can't report that its paper was later corrected, which two of these were. Full reasoning, the access-state table, and the per-entry procedure for adding one are in docs/RESOURCES-POLICY.md.

Slugs survive as anchors: /resources#<slug> is a permanent address for a single citation — and since 2026-08-18 that is where every [13] in the protocol points. The index points back: each entry names the sections that cite it, so you can see what a source is holding up rather than only that it was read. The manifest moved out of the page into src/Citations.elm at the same time, because §12's reference list had been a second hand-written copy of the same nineteen entries and the two had drifted on which papers carry corrections.

Docs

Doc	Owns
docs/autophagy-protocol.html	The source content (Rev. 3) — src/Page/Protocol.elm is its faithful translation
docs/DESIGN-REQUIREMENTS.md	Look, feel, voice, type, color, hard constraints
docs/DESIGN-PRINCIPLES.md	Layout structure, Elm structure, the print strategy
docs/RESOURCES-POLICY.md	The source index: link-first policy, access states, slugs
docs/DEPLOY.md	Cloudflare Pages pipeline, the 404 contract, cache policy, one-time setup
docs/20260816-theme-plan.md	The light/dark theme plan — closed, except the optional volt glow
AGENTS.md (CLAUDE.md)	The condensed brief for coding agents

Design decisions are amended in place, dated, in the doc that owns them.

Notes for contributors

• vite.config.js carries two deliberate workarounds: an HMR-accept rewrite for vite-plugin-elm under Vite 8, and a pinned cssTarget so minified range media queries stay parseable on pre-16.4 iOS WebKit. Both are commented at the source.
• package.json exists only to force cross-spawn@^6.0.6 through overrides, clearing a ReDoS advisory that vite-plugin-elm's dependency chain hard-pins with no upstream release to move to. deno.json has no equivalent mechanism, and Deno does read the field — without that file the vulnerable 6.0.5 is what gets installed. Do not delete it, and do not put dependencies or scripts in it; those live in deno.json.
• elm-test-rs is pinned to a fork. Upstream's Deno support dates from 2021 and calls three APIs Deno 2 removed, so --deno fails outright on stock 3.2.0. The fork is that fix and nothing else — see mise.toml.