docs: the wiki pointer, differential abundance documentation, and the community files

.editorconfig

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+# SPDX-License-Identifier: AGPL-3.0-only
+# SPDX-FileCopyrightText: 2026 Jonathan D.A. Jewell (hyperpolymath) <j.d.a.jewell@open.ac.uk>
+#
+# Editor configuration for this repository. The Julia sources indent with four
+# spaces, the frontend with two, YAML with two, and every text file ends with
+# a newline and no trailing whitespace.
+
+root = true
+
+[*]
+charset = utf-8
+end_of_line = lf
+insert_final_newline = true
+trim_trailing_whitespace = true
+
+[*.jl]
+indent_style = space
+indent_size = 4
+
+[*.{jl}]
+max_line_length = off
+
+[{*.ts,*.tsx,*.js,*.jsx,*.json,*.css,*.html}]
+indent_style = space
+indent_size = 2
+
+[{*.yml,*.yaml,*.kyaml}]
+indent_style = space
+indent_size = 2
+
+[*.md]
+indent_style = space
+indent_size = 2
+# Markdown's hard line breaks are two trailing spaces; keep them.
+trim_trailing_whitespace = false
+
+[Makefile]
+indent_style = tab
+
+[Justfile]
+indent_style = space
+indent_size = 4

.github/CODE_OF_CONDUCT.md

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+# Contributor Covenant Code of Conduct
+
+## Our Pledge
+
+We as members, contributors, and leaders pledge to make participation in our community a harassment-free experience for everyone, regardless of age, body size, visible or invisible disability, ethnicity, sex characteristics, gender identity and expression, level of experience, education, socio-economic status, nationality, personal appearance, race, caste, color, religion, or sexual identity and orientation.
+
+We pledge to act and interact in ways that contribute to an open, welcoming, diverse, inclusive, and healthy community.
+
+## Our Standards
+
+Examples of behavior that contributes to a positive environment for our community include:
+
+* Demonstrating empathy and kindness toward other people
+* Being respectful of differing opinions, viewpoints, and experiences
+* Giving and gracefully accepting constructive feedback
+* Accepting responsibility and apologizing to those affected by our mistakes, and learning from the experience
+* Focusing on what is best not just for us as individuals, but for the overall community
+
+Examples of unacceptable behavior include:
+
+* The use of sexualized language or imagery, and sexual attention or advances of any kind
+* Trolling, insulting or derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or email address, without their explicit permission
+* Other conduct which could reasonably be considered inappropriate in a professional setting
+
+## Enforcement Responsibilities
+
+Community leaders are responsible for clarifying and enforcing our standards of acceptable behavior and will take appropriate and fair corrective action in response to any behavior that they deem inappropriate, threatening, offensive, or harmful.
+
+Community leaders have the right and responsibility to remove, edit, or reject comments, commits, code, wiki edits, issues, and other contributions that are not aligned to this Code of Conduct, and will communicate reasons for moderation decisions when appropriate.
+
+## Scope
+
+This Code of Conduct applies within all community spaces, and also applies when an individual is officially representing the community in public spaces. Examples of representing our community include using an official e-mail address, posting via an official social media account, or acting as an appointed representative at an online or offline event.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be reported to the community leaders responsible for enforcement: the maintainer, [@JoshuaJewell](https://github.com/JoshuaJewell), using the contact details on their GitHub profile. All complaints will be reviewed and investigated promptly and fairly.
+
+All community leaders are obligated to respect the privacy and security of the reporter of any incident.
+
+## Enforcement Guidelines
+
+Community leaders will follow these Community Impact Guidelines in determining the consequences for any action they deem in violation of this Code of Conduct:
+
+### 1. Correction
+
+**Community Impact**: Use of inappropriate language or other behavior deemed unprofessional or unwelcome in the community.
+
+**Consequence**: A private, written warning from community leaders, providing clarity around the nature of the violation and an explanation of why the behavior was inappropriate. A public apology may be requested.
+
+### 2. Warning
+
+**Community Impact**: A violation through a single incident or series of actions.
+
+**Consequence**: A warning with consequences for continued behavior. No interaction with the people involved, including unsolicited interaction with those enforcing the Code of Conduct, for a specified period of time. This includes avoiding interactions in community spaces as well as external channels like social media. Violating these terms may lead to a temporary or permanent ban.
+
+### 3. Temporary Ban
+
+**Community Impact**: A serious violation of community standards, including sustained inappropriate behavior.
+
+**Consequence**: A temporary ban from any sort of interaction or public communication with the community for a specified period of time. No public or private interaction with the people involved, including unsolicited interaction with those enforcing the Code of Conduct, is allowed during this period. Violating these terms may lead to a permanent ban.
+
+### 4. Permanent Ban
+
+**Community Impact**: Demonstrating a pattern of violation of community standards, including sustained inappropriate behavior, harassment of an individual, or aggression toward or disparagement of classes of individuals.
+
+**Consequence**: A permanent ban from any sort of public interaction within the community.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage], version 2.1, available at [https://www.contributor-covenant.org/version/2/1/code_of_conduct.html][v2.1].
+
+Community Impact Guidelines were inspired by [Mozilla's code of conduct enforcement ladder][Mozilla CoC].
+
+For answers to common questions about this code of conduct, see the FAQ at [https://www.contributor-covenant.org/faq][FAQ]. Translations are available at [https://www.contributor-covenant.org/translations][translations].
+
+[homepage]: https://www.contributor-covenant.org
+[v2.1]: https://www.contributor-covenant.org/version/2/1/code_of_conduct.html
+[Mozilla CoC]: https://github.com/mozilla/diversity
+[FAQ]: https://www.contributor-covenant.org/faq
+[translations]: https://www.contributor-covenant.org/translations

.github/ISSUE_TEMPLATE/bug_report.yml

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+name: Bug report
+description: Something in MetaManifold does not work as documented.
+labels: [bug]
+body:
+  - type: markdown
+    attributes:
+      value: |
+        Search the existing issues first. Raise issues about a fork's own code on that fork.
+  - type: textarea
+    id: steps
+    attributes:
+      label: Steps or command
+      description: The command you ran, or the steps in the web interface, so that someone else can repeat them.
+    validations:
+      required: true
+  - type: textarea
+    id: expected
+    attributes:
+      label: What you expected
+    validations:
+      required: true
+  - type: textarea
+    id: actual
+    attributes:
+      label: What happened
+      description: Include the error message, the server log lines, or a screenshot.
+    validations:
+      required: true
+  - type: input
+    id: julia
+    attributes:
+      label: Julia version
+      placeholder: output of `julia --version`
+    validations:
+      required: true
+  - type: input
+    id: r
+    attributes:
+      label: R version
+      description: Only if the problem touches the R runtime; leave empty if you do not know it.
+      placeholder: output of `R --version | head -1`
+  - type: input
+    id: browser
+    attributes:
+      label: Browser and version
+      description: Only for problems in the web interface; leave empty for command-line reports.
+  - type: input
+    id: commit
+    attributes:
+      label: MetaManifold commit
+      placeholder: output of `git rev-parse --short HEAD`
+  - type: textarea
+    id: config
+    attributes:
+      label: Relevant configuration
+      description: The keys from `pipeline.yml` or the run's `run_config.yml` that bear on the problem.
+      render: yaml

.github/ISSUE_TEMPLATE/feature_request.yml

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+name: Feature request
+description: Suggest a new feature or a change to an existing one.
+labels: [enhancement]
+body:
+  - type: markdown
+    attributes:
+      value: |
+        Search the existing issues first. To change an architectural decision, describe the change
+        here before writing any code. The settled decisions in CONTRIBUTING.md can be discussed in an
+        issue, but a pull request does not reopen them.
+  - type: textarea
+    id: problem
+    attributes:
+      label: Problem
+      description: What you are trying to do, and what stops you now.
+    validations:
+      required: true
+  - type: textarea
+    id: proposal
+    attributes:
+      label: Proposed change
+      description: What MetaManifold should do instead. For a statistical method, name the method and a reference for it.
+    validations:
+      required: true
+  - type: textarea
+    id: alternatives
+    attributes:
+      label: Alternatives considered
+  - type: dropdown
+    id: area
+    attributes:
+      label: Area
+      options:
+        - Pipeline stages
+        - Analysis and statistics
+        - Web interface
+        - Configuration
+        - Installation and toolchain
+        - Other
+    validations:
+      required: true

.github/SECURITY.md

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+<!--
+SPDX-License-Identifier: AGPL-3.0-only
+SPDX-FileCopyrightText: 2026 Jonathan D.A. Jewell (hyperpolymath) <j.d.a.jewell@open.ac.uk>
+-->
+
+# Security policy
+
+## Deployment model, stated first
+
+MetaManifold is a **single-user, no-authentication** application: a Julia
+server with a browser UI, designed to run on localhost or on a host trusted
+by its one operator. The server carries real defences — a browser-origin
+allowlist with a DNS-rebinding check, strict Host checking on loopback binds,
+inert serving of uploaded report files, and Oxygen's docs and metrics pages
+switched off — but **exposing it beyond its intended deployment is the
+operator's risk, not a supported configuration.** Denial-of-service against
+an internet-exposed instance is out of scope, as is anything that follows
+from putting an unauthenticated API on a public network after ignoring the
+deployment guidance in the README's *Deployment* section.
+
+## What is in scope
+
+- The HTTP surface: the origin allowlist and Host checks
+  (`src/server/server.jl`), the static-file and report-upload serving
+  (`_file_middleware`), SPA routing, and every route under
+  `src/server/routes/`.
+- How configuration and primer values reach the external tools: pipeline
+  options and filenames become command lines; injection through them is a
+  finding here.
+- Path handling: the file routes, report item paths, and study/run names as
+  path components.
+- Installer and toolchain integrity: every download is SHA256-pinned
+  (`config/defaults/tool_versions.yml`); a tampered pin, an unchecked
+  substitute, or a way to make the installer fetch unverified content is a
+  finding.
+- Provenance integrity: `attestation.yml` and the content hashes it records;
+  anything that can make a run attest to bytes it did not use.
+- The dependency manifests: `Manifest.toml`, `renv.lock`, `frontend/bun.lock`.
+
+## What is out of scope
+
+- Vulnerabilities **in the external tools themselves** (cutadapt, FastQC,
+  MultiQC, DADA2, swarm, vsearch, cd-hit-est, MAFFT, trimAl, IQ-TREE, RAxML,
+  gappa, and the R packages): report those to their own projects. A way this
+  repository invokes them unsafely is in scope; their internal bugs are not.
+- Julia, R, bun and DuckDB runtime CVEs: report upstream; this project pins
+  versions and will pick up fixes through its normal dependency updates.
+- Internet-exposed DoS, as above.
+
+## Supported versions
+
+The default branch only. There are no backported releases; a fix lands on
+`main` behind the usual CI gates. The version that matters for any report is
+the git commit plus the pinned toolchain — and every run records exactly that
+in its `attestation.yml`.
+
+## How to report
+
+**Preferred channel: private vulnerability reporting.** The repository has
+it enabled; the *Report a vulnerability* button on the Security tab reaches
+the maintainers privately. Use it.
+
+**By email:** contact **developer@joshuajewell.dev** (Jonathan Jewell, the project
+owner) with `[security]` in the subject line.
+
+Include, where they apply:
+
+- what you found, and the impact you think it has;
+- the endpoint, route, or pipeline stage it affects;
+- the deployment mode — localhost, SSH tunnel, or split frontend/API;
+- reproduction steps, or the request that triggers it;
+- the versions block from the affected run's `attestation.yml` — it names the
+  exact commit and toolchain, which usually settles the first two replies.
+
+Reports are acknowledged when triaged, fixed on `main` with the normal CI
+gates, and disclosed on the reporter's preferred schedule. Credit is offered
+unless you prefer otherwise.
+
+## Mathematical foundations
+
+This project carries machine-checked proofs of some of its statistics, and it
+treats **unsound mathematics as a reportable weakness of its own kind**: a
+proof that is vacuous, a theorem that does not say what the code relies on, or
+a statistical claim the arithmetic does not support. If you find one, that is
+a finding — send it to **j.d.a.jewell@open.ac.uk**, where the
+proof-theoretic side of the project lives. Questions and open debate about
+the foundations belong in the
+[mathematical foundations discussion](https://github.com/hyperpolymath/MetaManifold-WebUI/discussions/149);
+private concerns about soundness belong in a report.

.github/dependabot.yml

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+# Dependabot version updates. Until this file landed, only security updates
+# ran (those need no configuration), and those failed for a separate reason:
+# the "Dependabot Updates" runs of 2026-09-26..27 tried to fix alerts against
+# fixtures under test/doi using the npm_and_yarn updater, which refuses a
+# Bun-managed project ("bun.lock but no package-lock.json"). Those fixtures
+# have since left the repository and both alerts are fixed.
+#
+# What cannot be covered here: Julia (Project.toml / Manifest.toml) and R
+# (renv.lock) are not Dependabot package-ecosystems. Their pins live in
+# config/defaults/tool_versions.yml and are asserted by
+# test/unit/test_install_pins.jl and the CI workflow instead.
+#
+# The workflows pin every action to a full commit SHA (this account's
+# allowlist policy, asserted by test/unit/test_install_pins.jl). Dependabot
+# advances those pins to the current SHA of the tracked version, so the
+# pinning policy itself survives updates.
+#
+# The #124 rule: minor and patch updates are batched, because they are
+# interchangeable in kind; a MAJOR (React 18->19, vite 6->8, TypeScript
+# 5->7 -- which #124 landed as one grouped PR, with the build already red
+# until #140 repaired it) is a migration, not an update. Every group below
+# therefore names its update-types as minor and patch ONLY: an update that
+# matches no group opens its own PR, carrying its own review and its own CI
+# run. test/unit/test_install_pins.jl asserts this shape, so a new group
+# cannot silently go back to batching majors.
+version: 2
+updates:
+  # The frontend is Bun-managed: package.json plus bun.lock, no npm/yarn/pnpm
+  # lockfile, so it must be declared as the "bun" ecosystem.
+  - package-ecosystem: "bun"
+    directory: "/frontend"
+    schedule:
+      interval: "weekly"
+    commit-message:
+      prefix: "chore(deps)"
+    groups:
+      # Minor and patch in one weekly PR; majors arrive one PR each.
+      frontend-minor-and-patch:
+        patterns: ["*"]
+        update-types: ["minor", "patch"]
+
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "weekly"
+    commit-message:
+      prefix: "chore(deps)"
+    groups:
+      # Same rule as the frontend: a new major of an action (checkout
+      # v4.4.0 -> v7.0.1 came through #123) gets a PR of its own.
+      actions-minor-and-patch:
+        patterns: ["*"]
+        update-types: ["minor", "patch"]