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backend/cli: CLI, server, agent runtime, tools

backend/cli/src/science: scientific database connectors

frontend/desktop: the Electron shell

Documentation site and repo docs

Release, packaging, and publish workflows

backend/cli/skills: bundled skill library

frontend/workspace: the browser UI

Something isn't working

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Dead-code removal

Files no entry point reaches

Proposed removal; review its scope

Documentation and artifact retirement proposals requiring owner confirmation

Code analysis supports this removal

Exports referenced nowhere

Module-private declarations nothing references

Pull requests that update a dependency file

Improvements or additions to documentation

This issue or pull request already exists

New feature or request

Pull requests that update GitHub Actions code

Good for newcomers

Extra attention is needed

This doesn't seem right

Pull requests that update javascript code

New issue awaiting maintainer triage