fix(agents-init): clean up stale anchored gitignore patterns on migration

functions/agents-init.fish

@@ -247,6 +247,29 @@ function agents-init --description 'scaffold AGENTS/ sub-repo with agent spec fi
             end
         end
 
+        # ── Migrate stale anchored gitignore lines ──────────────────────────────
+        # A project scaffolded by the old agents-init already has anchored
+        # /AGENTS.md and/or /CLAUDE.md lines in .gitignore. git check-ignore
+        # sees those as covering the literal path "AGENTS.md", so the new
+        # unanchored pattern below would be judged already-covered and never
+        # added -- leaving any newly discovered subdirectory AGENTS.md with no
+        # gitignore coverage at all. Strip the stale exact lines first so the
+        # unanchored pattern always gets a chance to be added. No-op when
+        # neither stale line is present.
+        set -l gitignore "$root/.gitignore"
+        if test -f "$gitignore"
+            if grep -qxF "/AGENTS.md" "$gitignore"
+                sed -i '/^\/AGENTS\.md$/d' "$gitignore"
+                set changed 1
+                test $verbose -eq 1; and echo "$c_warn→ Removed stale /AGENTS.md line from .gitignore$c_reset"
+            end
+            if grep -qxF "/CLAUDE.md" "$gitignore"
+                sed -i '/^\/CLAUDE\.md$/d' "$gitignore"
+                set changed 1
+                test $verbose -eq 1; and echo "$c_warn→ Removed stale /CLAUDE.md line from .gitignore$c_reset"
+            end
+        end
+
         # ── .gitignore ────────────────────────────────────────────────────────
         # Unanchored: matches AGENTS.md at every depth, so a newly
         # discovered subdirectory needs no additional gitignore entry.

tests/test-agents-init.fish

@@ -199,5 +199,21 @@ check "inversion fix: mirror CLAUDE.md gone" false (test -e $e2/AGENTS/docs/CLAU
 check "inversion fix: project docs/AGENTS.md relinked directly" ../AGENTS/docs/AGENTS.md (readlink $e2/docs/AGENTS.md)
 check "inversion fix: project docs/CLAUDE.md gone" false (test -e $e2/docs/CLAUDE.md; and echo true; or echo false)
 
+echo ""
+echo "== agents-init: stale anchored gitignore lines migrated =="
+
+set -l e3 (new_repo)
+mkdir -p $e3/AGENTS
+echo real-agents >$e3/AGENTS/AGENTS.md
+ln -s AGENTS/AGENTS.md $e3/AGENTS.md
+printf '%s\n' AGENTS/ "/AGENTS.md" "/CLAUDE.md" >$e3/.gitignore
+pushd $e3 >/dev/null
+set -l ercD (agents-init --agents --silent 2>/dev/null; echo $status)
+popd >/dev/null
+check "stale gitignore: exits 0" 0 "$ercD"
+check "stale gitignore: anchored /AGENTS.md line removed" false (grep -qxF '/AGENTS.md' $e3/.gitignore; and echo true; or echo false)
+check "stale gitignore: anchored /CLAUDE.md line removed" false (grep -qxF '/CLAUDE.md' $e3/.gitignore; and echo true; or echo false)
+check "stale gitignore: unanchored AGENTS.md pattern present" true (grep -qxF 'AGENTS.md' $e3/.gitignore; and echo true; or echo false)
+
 cleanup
 report