Initial analysis

.gitignore

@@ -1,2 +1,3 @@
 tmp
 analysis/venv
+.aider*

analysis/README.md

@@ -46,6 +46,8 @@ The result was a CSV-formatted list of protocols (`protocols_edited.csv`, n=411)
 
 ### Initial diagnostic
 
+This diagnostic used the file now at `bicorder_analyzed.json`, though the scripts are set up to analyze `../bicorder.json`. That file has since been updated based on this analysis.
+
 For each row in the dataset, and on each gradient, a series of scripts prompts the LLM to apply each gradient to the protocol. The outputs are then added to a CSV output file.
 
 The result was a CSV-formatted list of protocols (`diagnostic_output.csv`, n=411).