Write down the conventions plugins here share

[Marius1311]

Adds a Conventions section to the README, so a new plugin can follow the rules before its PR rather than learn them in review (#12). Anything the section doesn't cover stays the plugin's own choice.

• Overlap and dependencies. Overlapping and alternative plugins are welcome, and each one's README says how it differs from the plugins it overlaps with. A plugin that builds on another defers to it rather than restating it. One that needs another to work declares it in dependencies, which installs both (tested with a throwaway marketplace), and its Develop section says to load both.
• Little always-on context. Rules go in skills. Hooks only for what must hold in every session, since their output adds up across installed plugins.
• One project layout. AGENTS.md (Claude Code and Codex both read it, docs) and .claude/worktrees/.
• Repository and release. The README layout and version-bump releases, moved here from the closing paragraph, plus claude plugin validate ., userConfig for per-person values, and nothing private in public text.

The four listed plugins pass claude plugin validate. cell-type-annotation declares its dependencies in quadbio/cell-type-annotation#55.

🤖 Generated with Claude Code

https://claude.ai/code/session_01Cu5AYoH46bk3rW3qivyPZ5

[chatgpt-codex-connector]

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Review	Status	Commit	Review trigger
📝 Code Review	✅ Completed 2026-10-13T18:47:44.996509Z	a4db3c2	New commits

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[Marius1311]

Conventions needs a bit or revising to be appropriate for a lab's central place for plugins. If it was only my own plugins, it would be okay to say we have only one way of doing things, and plugins strictly build on each other, but with several people contributing, we need to adopt a bit.

[Marius1311]

I think that's overly strict. If we want this marketplace to become the central hub for quadbio plugins, we need to be open to alternative working styles, i.e. plugins that might mix analysis setup with another aim.

I agree with the other conventions below, just this one needs updating. As another example, someone might contribute an alternative euler-hpc skill, with a different recommended way of working. That's okay, we can accomodate different alternatives in the marketplace.

Later on, once we have more plugins, we could group them around common themes, to emphasize structure and organization.

[Marius1311]

Agreed, fixed in a4db3c2. The block is now "Overlap and dependencies": overlapping and alternative plugins are welcome, and each one's README names the plugins it overlaps with and how it differs, so users can choose. What stays is for plugins that build on another: defer instead of restating, and declare dependencies when it needs the other to work. I dropped "one concern per plugin" and the trigger rule. Grouping by theme can come once the table grows.

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Reviewed commit: a4db3c2fc9

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[chatgpt-codex-connector]

Ignore the in-repository worktree directory

For any plugin repository without an existing ignore rule, following this convention makes claude --worktree create a nested checkout that appears as an untracked .claude/worktrees/<name>/ tree in the main checkout, leaving git status dirty and making accidental staging possible. The official --worktree documentation explicitly says to add .claude/worktrees/ to .gitignore, so this shared layout convention should require that rule as well.

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[Marius1311]

Fixed in 561ff56: the rule now says .gitignore lists .claude/worktrees/, and this repo gets that .gitignore. cell-type-annotation was the only plugin missing it; added in quadbio/cell-type-annotation#55.