Development History and Principles

"A scientific judgment call is not a thing to automate — not by me, and not by anything I hand the work to."

Most of this manual is about running PoolSeqFlow. This section is about how it is built, who builds it, and why it takes the form it does.

That is in the manual rather than in a README because it is a user's question, not a developer's. If you are going to base results on a tool, it matters whether anyone is still maintaining it, what happens when a method it implements is superseded, who checks that a change did not quietly alter a number, and how much of it and what parts of it was written with an AI agent and under what review. Those are all reasonable things to want answered before you commit an experiment to it, and none of them is answered by the parameter reference.

Four pages, and they are meant to be read in order:

• History — who wrote what, and when. It starts here because the commit log gives the wrong answer on its own.
• Rationale — why this is a maintained tool rather than a paper, how I decide things, and who the tool is for.
• Verification — what stops a change being wrong. This is what makes the rest of the section checkable rather than something to take on trust.
• Claude Code — what was done with an AI agent from v2.0.0 onward, what it got wrong, and what the arrangement demands of the person reviewing it.

"I am not claiming using an AI agent is a way to build something you do not understand. It is a way to build something you do understand, faster, if you are willing to spend the time saved on reading what's built."