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Shrink for Github - A macOS app for your Github issues
Freeplane - Freeplane is a powerful and free software for building mind maps.
GitHub Reader - A quick way to browse GitHub issues and pull requests.
vym - VYM (View Your Mind) is a tool to generate and manipulate maps which show your thoughts.
Codetree - You can manage your entire development process through GitHub.
Linked Ideas - A macOS/iOS apps to treat ideas as links of concepts.