diff --git a/functions/_agents_init_ensure_gitignore.fish b/functions/_agents_init_ensure_gitignore.fish
index 724af70..f1f5549 100644
--- a/functions/_agents_init_ensure_gitignore.fish
+++ b/functions/_agents_init_ensure_gitignore.fish
@@ -7,7 +7,7 @@
 # DESCRIPTION
 #   Appends any patterns not already covered by the project's .gitignore.
 #   Uses git check-ignore for accurate rule matching (catches wildcards
-#   and parent-dir globs). Falls back to a plain string search when the
+#   and parent-dir globs). Falls back to a whole-line string search when the
 #   root is not a git repository. Leading / is stripped from each pattern
 #   before the path-based check so root-anchored patterns (e.g. /AGENTS.md)
 #   are matched correctly.
@@ -58,7 +58,9 @@ function _agents_init_ensure_gitignore
             git -C "$root" check-ignore -q --no-index "$check_path" 2>/dev/null
             and set already 1
         else if test -f "$gitignore"
-            grep -qF "$pattern" "$gitignore"
+            # Whole-line match: a substring match treats a negation line
+            # such as "!AGENTS/foo" as covering the pattern "AGENTS/".
+            grep -qxF "$pattern" "$gitignore"
             and set already 1
         end
         if test $already -eq 0
diff --git a/functions/agents-init.fish b/functions/agents-init.fish
index ca36e19..539e4ef 100644
--- a/functions/agents-init.fish
+++ b/functions/agents-init.fish
@@ -17,6 +17,11 @@
 #   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)
@@ -127,9 +132,20 @@ function agents-init --description 'scaffold AGENTS/ sub-repo with agent spec fi
     end
     # --verbose is explicit default; no-op but accepted for completeness
 
-    # Resolve target root: git root if available, otherwise cwd
+    # Only scaffold inside a git repository, or where an agent file already
+    # exists. Falling back to (pwd) meant `claude --version` in any
+    # directory created an AGENTS/ repo, two root symlinks, and a docs/
+    # tree there.
     set -l root (git rev-parse --show-toplevel 2>/dev/null)
-    test -z "$root"; and set root (pwd)
+    if test -z "$root"
+        if test -e (pwd)/AGENTS.md -o -e (pwd)/CLAUDE.md -o -d (pwd)/AGENTS
+            set root (pwd)
+        else
+            test $verbose -eq 1
+            and echo "$c_dim→ Not a git repository; skipping AGENTS/ scaffolding$c_reset"
+            return 0
+        end
+    end
 
     set -l agents_dir "$root/AGENTS"
     set -l plugins_dir "$agents_dir/plugins"
diff --git a/tests/test-agents-vault.fish b/tests/test-agents-vault.fish
index 9a92f0b..972b0bc 100644
--- a/tests/test-agents-vault.fish
+++ b/tests/test-agents-vault.fish
@@ -2053,6 +2053,38 @@ check "agents-init: a rejected commit returns non-zero" 1 "$ibrc"
 check "agents-init: a rejected commit says nothing was recorded" true (string match -q '*nothing recorded*' -- (cat $ierr); and echo true; or echo false)
 check "agents-init: a rejected commit really recorded nothing" $ibhead (git -C $ip/AGENTS rev-list --count HEAD)
 
+#   ─────────────────────── scaffolding guard ──────────────────────────────
+# Resolving the root to (pwd) meant running an agent CLI in any directory
+# created an AGENTS/ repo, root symlinks and a docs/ tree there.
+echo ""
+echo "== agents-init scaffolding guard =="
+
+set -l plain (mktemp -d)
+set -ga TMPDIRS $plain
+pushd $plain >/dev/null
+agents-init --silent 2>/dev/null
+popd >/dev/null
+check "no scaffold in a non-git dir" false (test -e $plain/AGENTS; and echo true; or echo false)
+
+# A pre-existing agent file still opts the directory in.
+set -l plainagents (mktemp -d)
+set -ga TMPDIRS $plainagents
+touch $plainagents/AGENTS.md
+pushd $plainagents >/dev/null
+agents-init --silent 2>/dev/null
+popd >/dev/null
+check "an existing AGENTS.md still scaffolds" true (test -d $plainagents/AGENTS; and echo true; or echo false)
+
+#   ──────────────────── gitignore fallback anchoring ──────────────────────
+echo ""
+echo "== gitignore fallback anchoring =="
+
+set -l ng (mktemp -d)
+set -ga TMPDIRS $ng
+printf '!AGENTS/foo\n' >$ng/.gitignore
+_agents_init_ensure_gitignore $ng "test" "AGENTS/" >/dev/null
+check "negation does not count as ignored" true (grep -qx 'AGENTS/' $ng/.gitignore; and echo true; or echo false)
+
 #   ──────────────────────── hermeticity assertion ────────────────────────
 # The whole suite must never have touched the real global agent state. The
 # failure this guards is specific: a global-memory sync with no test