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

.github/CODE_OF_CONDUCT.md

@@ -0,0 +1,83 @@
+# 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

CONTRIBUTING.md → .github/CONTRIBUTING.md

@@ -98,7 +98,7 @@ A pull request does not reopen these. An issue can discuss them.
 
 - `config/defaults/tool_versions.yml` pins Julia, R, bun and the external tools,
   and `install.jl` and CI both install from it. The Julia version is repeated in
-  the CI matrix. Change a pin by editing that file, and expect the change to be
+  the CI workflow. Change a pin by editing that file, and expect the change to be
   discussed.
 - R packages are pinned in `renv.lock`.
 - CI job names carry no version numbers, so that a pin change leaves required

.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
+      placeholder: output of `R --version | head -1`
+    validations:
+      required: true
+  - type: input
+    id: browser
+    attributes:
+      label: Browser and version
+    validations:
+      required: true
+  - 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

@@ -0,0 +1,41 @@
+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/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.
+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:
+      frontend:
+        patterns: ["*"]
+
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "weekly"
+    commit-message:
+      prefix: "chore(deps)"
+    groups:
+      actions:
+        patterns: ["*"]

.github/pull_request_template.md

@@ -0,0 +1,43 @@
+## Summary
+
+<!-- What does this PR do, and why? One logical change per PR. -->
+
+Closes #
+
+## Type of change
+
+- [ ] 🐛 Bug fix (non-breaking change that fixes an issue)
+- [ ] ✨ New feature (non-breaking change that adds functionality)
+- [ ] 💥 Breaking change (would change existing behaviour, a config key or an API response)
+- [ ] 📊 Statistics fix (a method returned a wrong number, or a result it could not support)
+- [ ] 📖 Documentation
+- [ ] 🧹 Refactor / tech debt (behaviour-preserving)
+- [ ] ⚡ Performance
+- [ ] 🔧 Build / CI / tooling
+
+## How has this been verified?
+
+<!-- Name the commands you ran and what they reported. For example:
+     julia --project=. test/runtests.jl
+     julia --project=. -t 2 test/runtests.jl --integration --server
+     cd frontend && bun run test -->
+
+Tested with Julia `…`, R `…` and bun `…`.
+
+## What this leaves out
+
+<!-- Anything related that this PR does not do, and why. -->
+
+## Checklist
+
+- [ ] My branch starts at the current tip of `main` (`behind_by` is `0`; see CONTRIBUTING.md) and has no merge commits from `main`.
+- [ ] I ran `julia --project=. test/runtests.jl` (and `cd frontend && bun run test` for frontend changes) and they pass.
+- [ ] CI ran on this PR and passes.
+- [ ] No generated or vendored files, and no lockfile change the work does not need (or the reason is given above).
+- [ ] New code is AGPL-3.0, or MPL-2.0 with an SPDX identifier in each file I wrote. I left existing file headers, `LICENSE`, `CITATION.cff` and the licence and acknowledgement sections of `README.md` unchanged.
+- [ ] Every number shown to a user is computed from their data. When a method cannot run it raises an explicit error.
+- [ ] Docs are updated, and no claim in them overstates what the code does.
+
+## Notes for reviewers
+
+<!-- Anything that needs special attention, follow-up, or context. To be considered for authorship in CITATION.cff, say so here. -->