diff --git a/templates/agents-genome.md b/templates/agents-genome.md
index f9446d9..be09625 100644
--- a/templates/agents-genome.md
+++ b/templates/agents-genome.md
@@ -171,6 +171,8 @@ private: true | false
 
 ### Index entries
 
+> **Skill mode:** auto-generated by `run-ingest.sh` from manifest. Below applies to manual workflows only.
+
 Append at bottom of relevant section in `wiki/index.md`:
 
 ```
@@ -181,6 +183,8 @@ Never reorder. Alphabetical sort is handled by the pre-commit hook.
 
 ### Log entries
 
+> **Skill mode:** auto-generated by `run-ingest.sh` from manifest. Below applies to manual workflows only.
+
 Append one entry per operation to `wiki/log.md`:
 
 ```markdown