We're building a CAD for drug design, we often have to handle large and highly varied file formats. Protein structures, compounds, python scripts, lab notebook entries, instrumentation data, etc.
From a data structure and file ergonomics perspective, think of it as similar to Unity or UE4 for drug design. We have a huge variety of assets to manage alongside their relationships to each other, and the project files are local on the user's machine (with a collaboration / sync over the network between scientists working on the same project, hence where something like this would come in for us).
Many of those files are fine with a winning side strategy, but some of them might not be that clean. Take a protein structure defined by an `mmcif` file for example, if we clean the file by removing hydrogen atoms and another scientist repairs a side chain on that same file then we'd need a way to reconcile those differences.
On the agent side, our agents will generate small python scripts that manipulate the proteins, then cache and re-use those scripts as tools when possible. So preserving those scripts alongside the mutated asset and conversation history is something we've been working on.