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jonn-smithclaude
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chore: relicense to MIT (#6)
Switch the repo back to the MIT License (Copyright (c) 2025-2026 Broad Institute). Updates every reference to the prior PolyForm Shield 1.0.0 text across the repo so they stay consistent: - LICENSE: full MIT text - README.md: license section + repo-layout one-liner - CONTRIBUTING.md: contribution-licensing note - AGENTS.md: repo-layout one-liner + license bullet - docker/hvp-monolith/Dockerfile: comment above `COPY LICENSE` The image-bundling mechanism (`COPY LICENSE /opt/hvp-lr/LICENSE` in the Dockerfile, staged into the build context by the Makefile and the CI workflow) is unchanged — MIT also requires the notice + license text to travel with copies of the software. Co-authored-by: Jonn Smith <11667487+jonn-smith@users.noreply.github.com> Co-authored-by: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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AGENTS.md

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├── .pre-commit-config.yaml # WDL validation hook
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├── dev-requirements.txt # Local dev tooling (miniwdl, pre-commit)
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├── VERSION # Repo-level version bumped by cd.yml on each release
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├── LICENSE # PolyForm Shield 1.0.0 (bundled into every image)
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├── LICENSE # MIT License (bundled into every image)
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├── README.md # Human-facing orientation
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├── CONTRIBUTING.md # Setup + PR workflow (humans + agents)
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├── CLAUDE.md # Pointer for Claude sessions
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- [README.md](README.md) — short human-facing orientation.
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- [CONTRIBUTING.md](CONTRIBUTING.md) — setup + PR workflow shared by humans and agents.
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- [LICENSE](LICENSE)PolyForm Shield 1.0.0. Source-available, not OSI open source.
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- [LICENSE](LICENSE)MIT License.
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- `.github/workflows/docker.yml` and `.github/workflows/cd.yml` — the source of truth for everything described above. If this file ever drifts from those workflows, the workflows win.
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- `scripts/ci-detect-changed-images.sh`, `scripts/ci-bump-image-versions.sh` — CI internals; do not invoke directly.

CONTRIBUTING.md

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## License
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Contributions are accepted under [PolyForm Shield 1.0.0](LICENSE) (source-available, not OSI open source). The license file is bundled into every built container at `/opt/hvp-lr/LICENSE`.
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Contributions are accepted under the [MIT License](LICENSE). The license file is bundled into every built container at `/opt/hvp-lr/LICENSE`.

LICENSE

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# PolyForm Shield License 1.0.0
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<https://polyformproject.org/licenses/shield/1.0.0>
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Required Notice: Copyright (c) 2025-2026 Broad Institute
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## Acceptance
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In order to get any license under these terms, you must agree to them as both strict obligations and conditions to all your licenses.
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## Copyright License
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The licensor grants you a copyright license for the software to do everything you might do with the software that would otherwise infringe the licensor's copyright in it for any permitted purpose. However, you may only distribute the software according to [Distribution License](#distribution-license) and make changes or new works based on the software according to [Changes and New Works License](#changes-and-new-works-license).
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## Distribution License
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The licensor grants you an additional copyright license to distribute copies of the software. Your license to distribute covers distributing the software with changes and new works permitted by [Changes and New Works License](#changes-and-new-works-license).
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## Notices
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You must ensure that anyone who gets a copy of any part of the software from you also gets a copy of these terms or the URL for them above, as well as copies of any plain-text lines beginning with `Required Notice:` that the licensor provided with the software. For example:
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> Required Notice: Copyright Yoyodyne, Inc. (http://example.com)
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## Changes and New Works License
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The licensor grants you an additional copyright license to make changes and new works based on the software for any permitted purpose.
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## Patent License
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The licensor grants you a patent license for the software that covers patent claims the licensor can license, or becomes able to license, that you would infringe by using the software.
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## Noncompete
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Any purpose is a permitted purpose, except for providing any product that competes with the software or any product the licensor or any of its affiliates provides using the software.
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## Competition
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Goods and services compete even when they provide functionality through different kinds of interfaces or for different technical platforms. Applications can compete with services, libraries with plugins, frameworks with development tools, and so on, even if they're written in different programming languages or for different computer architectures. Goods and services compete even when provided free of charge. If you market a product as a practical substitute for the software or another product, it definitely competes.
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## New Products
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If you are using the software to provide a product that does not compete, but the licensor or any of its affiliates brings your product into competition by providing a new version of the software or another product using the software, you may continue using versions of the software available under these terms beforehand to provide your competing product, but not any later versions.
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## Discontinued Products
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You may begin using the software to compete with a product or service that the licensor or any of its affiliates has stopped providing, unless the licensor includes a plain-text line beginning with `Licensor Line of Business:` with the software that mentions that line of business. For example:
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> Licensor Line of Business: YoyodyneCMS Content Management System (http://example.com/cms)
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## Sales of Business
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If the licensor or any of its affiliates sells a line of business developing the software or using the software to provide a product, the buyer can also enforce [Noncompete](#noncompete) for that product.
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## Fair Use
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You may have "fair use" rights for the software under the law. These terms do not limit them.
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## No Other Rights
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These terms do not allow you to sublicense or transfer any of your licenses to anyone else, or prevent the licensor from granting licenses to anyone else. These terms do not imply any other licenses.
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## Patent Defense
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If you make any written claim that the software infringes or contributes to infringement of any patent, your patent license for the software granted under these terms ends immediately. If your company makes such a claim, your patent license ends immediately for work on behalf of your company.
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## Violations
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The first time you are notified in writing that you have violated any of these terms, or done anything with the software not covered by your licenses, your licenses can nonetheless continue if you come into full compliance with these terms, and take practical steps to correct past violations, within 32 days of receiving notice. Otherwise, all your licenses end immediately.
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## No Liability
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***As far as the law allows, the software comes as is, without any warranty or condition, and the licensor will not be liable to you for any damages arising out of these terms or the use or nature of the software, under any kind of legal claim.***
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## Definitions
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The **licensor** is the individual or entity offering these terms, and the **software** is the software the licensor makes available under these terms.
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A **product** can be a good or service, or a combination of them.
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**You** refers to the individual or entity agreeing to these terms.
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**Your company** is any legal entity, sole proprietorship, or other kind of organization that you work for, plus all its affiliates.
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**Affiliates** means the other organizations than an organization has control over, is under the control of, or is under common control with.
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**Control** means ownership of substantially all the assets of an entity, or the power to direct its management and policies by vote, contract, or otherwise. Control can be direct or indirect.
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**Your licenses** are all the licenses granted to you for the software under these terms.
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**Use** means anything you do with the software requiring one of your licenses.
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MIT License
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Copyright (c) 2025-2026 Broad Institute
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Permission is hereby granted, free of charge, to any person obtaining a copy
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of this software and associated documentation files (the "Software"), to deal
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in the Software without restriction, including without limitation the rights
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to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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copies of the Software, and to permit persons to whom the Software is
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furnished to do so, subject to the following conditions:
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The above copyright notice and this permission notice shall be included in all
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copies or substantial portions of the Software.
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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SOFTWARE.

README.md

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├── .pre-commit-config.yaml # WDL validation hook
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├── dev-requirements.txt # Local dev tooling
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├── VERSION # Repo-level version
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├── LICENSE # PolyForm Shield 1.0.0
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├── LICENSE # MIT License
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├── README.md # This file
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├── CONTRIBUTING.md # Setup + PR workflow
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├── CLAUDE.md # Pointer for Claude sessions
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## License
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PolyForm Shield 1.0.0 — see [LICENSE](LICENSE). Source-available, not OSI open source. Any use is permitted except providing a product that competes with HVP-LR or with software the Broad Institute provides using HVP-LR. The LICENSE file is bundled into every built container at `/opt/hvp-lr/LICENSE`.
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If you intend to redistribute an image or its derivatives, propagate the LICENSE and any `Required Notice:` lines per the Shield "Notices" section.
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MIT — see [LICENSE](LICENSE). The LICENSE file is bundled into every built container at `/opt/hvp-lr/LICENSE`. If you redistribute the source or an image, MIT requires the copyright notice and license text to travel with it.

docker/hvp-monolith/Dockerfile

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# PolyForm Shield 1.0.0 requires distributing the license with the software.
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# MIT requires the copyright notice + license text travel with copies of
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# the software. Bundle the repo-root LICENSE into the image.
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COPY LICENSE /opt/hvp-lr/LICENSE
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# Set working directory

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