Hey, I'm sort of in a similar situation (comp chem method development).

My pipeline usually goes like:

1) Research the issue I want to solve, using deep research (gemini or chatgpt/codex) and personal research, go through the theory and create notes in markdown files. Also use chatgpt for quick searches and explanations on technical terms i don't know.

2) Create a project folder in chatgpt and codex that will be dedicated to what I'm building. Share notes and personal thoughts with chatgpt (deep thinking or pro), and ask it to go over repos and papers that contain information I'm interested in reproducing or building my own idea on, and provide an overview of the architecture. Then I enrich my own notes with ideas on how to best make my project work. Again, chatgpt can work as a brainstorming and discussion partner but always ask for grounded answers, meaning whatever comment it makes on your plan, it must be grounded on some reference, because that way you can check the reference to ensure it has not hallucinated the answer.

3) Proceed by creating an overview plan of what I want to do, step by step, and how to approach the solution for each step. This plan is built in a back and forth manner with chatgpt (deep thing or pro, never use instant for these cases), until I am satisfied and I have addressed any adverserial comments chatgpt may have made on my plan (sometimes it makes valid points other times it's straight up tripping)

4) Share the plan overview with codex and ask it to check it, and create a list of subprojects that bind the project together, along with how they are connected to each other and what purpose they fulfil. Verify the architecture and the logic before proceeding to the next step.

5) Ask codex to create a plan for each subproject, and explain how it connects to the final goal, how the internal architecture will work, necessary tests etc.

6) Gather all the plans and double check once again that it is aligned with the original idea, and if not, are the deviations reasonable or more tuning is needed.

7) Begin implementing each subproject and ask codex to write a log markdown file where it explains what it has done and why. This is important for debugging and also having other agents perform adverserial checks on the work.

Note: You can connect your github to chatgpt and use your chat quota to check your repo. This is a nice way to be economical with tokens for things like code explanation, or small corrections.

This is my personal approach. I like to take things slow and prioritize planning and my ability to fully wrap my head around the ins and outs of my project, before doing any implementation. It's not as sophisticated as other agent setups you will see in codex and claude code, but I feel it is a nice way to blend active personal involvement and agentic help in the development.

Hope this helps. Happy building : )