IGVF-DACC / igvf-ui / #6186

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IGVF-2948 Replace d3-dag with ELK and React Flow (#878)

* Initial React Flow test implementation with three simple nodes.
* Introducing ELK for layout, but not actually using it yet.
* Implement custom nodes, invisible handles, and black edges and arrowheads. Still not using ELK.
* Add ELK layout to the React Flow graph.
* Display grouped nodes in the test graph.
* Clean up the appearance of the graph to be more balanced.
* Clean up the code.
* Rewrite function that converts ELK objects to React Flow objects so that it’s far simpler.
* A little extra cleanup.
* Move functions to convert ELK objects to React Flow arrays to components/file-graph/lib.ts.
* Testing prettier for pre-commit.
* Rendering a real file association graph with no file sets.
* Clean up all the errors in the code. Define new types for ELK and React Flow nodes to carry metadata through.
* Format the file nodes like they are in d3-dag. Remove now-unused prettier.config.js. Update .prettierrc to sort Tailwind CSS classes.
* Do some code clean up before starting on the file-set nodes.
* Add functionality to get all upstream file objects from any file in the graph. The function to trim isolated files now ignores any derived-from files not included in the native or external files, most likely because the user doesn’t have privileges to load them.
* Update utility functions for efficiency. Update comments.
* Add code to build the file-set nodes. Don’t do anything with it yet. The next step will update edge data with file sets.
* Revert to use file paths as file-node IDs to make it easier to find the corresponding file.
* File-set nodes now in the graph with appropriate edges.
* Refactor and clean up graph-generation code.
* Connect the modals to the file and file-set nodes. Move types to types.ts.
* Add colors to file-set nodes.
* Set the colors of the edges and markers using the Tailwind CSS color configuration. Set the colors of the file-set nodes and their borders, as well as the file... (continued)

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