diff --git a/docs/fish-config.1 b/docs/fish-config.1
index 65b75c6..5b6f1c8 100644
--- a/docs/fish-config.1
+++ b/docs/fish-config.1
@@ -2701,6 +2701,11 @@ a self-contained git repo for agent specifications, moves any existing
 agent-related files into it, and replaces them with symlinks so the outer
 project never tracks agent files directly.
 
+Scaffolding runs only inside a git repository, or in a directory that
+already has an AGENTS.md, CLAUDE.md, or AGENTS/. Elsewhere it is a
+no-op, so running an agent CLI in an arbitrary directory does not
+create a repository there.
+
 File layout after setup:
   AGENTS/AGENTS.md          canonical agent spec (real file)
   AGENTS/CLAUDE.md          real file (if CLAUDE.md existed separately)
diff --git a/docs/fish-config.md b/docs/fish-config.md
index b42e610..5472ad4 100644
--- a/docs/fish-config.md
+++ b/docs/fish-config.md
@@ -2175,6 +2175,11 @@ functions). They are active in all interactive sessions.
     agent-related files into it, and replaces them with symlinks so the outer
     project never tracks agent files directly.
 
+    Scaffolding runs only inside a git repository, or in a directory that
+    already has an AGENTS.md, CLAUDE.md, or AGENTS/. Elsewhere it is a
+    no-op, so running an agent CLI in an arbitrary directory does not
+    create a repository there.
+
     File layout after setup:
       AGENTS/AGENTS.md          canonical agent spec (real file)
       AGENTS/CLAUDE.md          real file (if CLAUDE.md existed separately)