[WIP] Review backend code and determine remaining work for project completion

[Copilot]

Thanks for asking me to work on this. I will get started on it and keep this PR's description up to date as I form a plan and make progress.

Original prompt

Review the back end code and determine what work is remaining to complete the project so that it is fully functional and complete. Trace each pipeline and make sure the application is fully unified, that unused files or code is removed, that there are no bugs or issues with the CLI, and integrate additional research database APIs if possible, along with web search functionality.

The system should be able to ingest any number of text based files within the input/ folder and the pipeline should ingest everything. It's likely that the context will be too big for the agents, so it will be important to chunk the files on the first pass and extract queryable insights that will be used to search research databases like arXiv.

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