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/tests/test-agents-vault.fish b/tests/test-agents-vault.fish
index 823d458..972b0bc 100644
--- a/tests/test-agents-vault.fish
+++ b/tests/test-agents-vault.fish
@@ -2075,6 +2075,16 @@ 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