diff --git a/.gitignore b/.gitignore
index ae8e047..82cafc1 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,2 +1,3 @@
 tmp
 analysis/venv
+.aider*
diff --git a/analysis/README.md b/analysis/README.md
index 445edb3..1d20ef2 100644
--- a/analysis/README.md
+++ b/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).
diff --git a/analysis/bicorder_analyze.py b/analysis/bicorder_analyze.py
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diff --git a/analysis/bicorder_batch.py b/analysis/bicorder_batch.py
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diff --git a/analysis/bicorder_init.py b/analysis/bicorder_init.py
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diff --git a/analysis/bicorder_query.py b/analysis/bicorder_query.py
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diff --git a/analysis/chunk.sh b/analysis/chunk.sh
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diff --git a/analysis/multivariate_analysis.py b/analysis/multivariate_analysis.py
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