Validate nested end markers are alone on their line

Extract isEndMarkerAloneOnLine helper and apply it to nested end
markers so trailing content like <?/mock?> extra emits a diagnostic
instead of silently decrementing depth. Add subdirectory recursive
expansion test proving no double-pathing occurs with RootFS=readFS.

https://claude.ai/code/session_01J3g8NnEwGYyJWXD1bqtTii

Author: claude

internal/archetype/gensection/engine_test.go

@@ -209,6 +209,24 @@ func TestEngine_Check_MalformedNestedEndMarker(t *testing.T) {
 		"expected malformed nested end marker diagnostic, got %v", diags)
 }
 
+func TestEngine_Check_NestedEndMarkerTrailingContent(t *testing.T) {
+	// A nested end marker with trailing content on its line should
+	// emit a diagnostic and not decrement depth.
+	src := "<?mock\nkey: a\n?>\n<?mock\nkey: b\n?>\ninner\n<?/mock?> extra\n<?/mock?>\n<?/mock?>\n"
+	f := newTestFile(t, "test.md", src)
+	d := &mockDirective{content: ""}
+	e := NewEngine(d)
+	diags := e.Check(f)
+	found := false
+	for _, d := range diags {
+		if strings.Contains(d.Message, "only content on its line") {
+			found = true
+		}
+	}
+	assert.True(t, found,
+		"expected 'only content on its line' diagnostic, got %v", diags)
+}
+
 func TestEngine_Check_InvalidYAML(t *testing.T) {
 	src := "<?mock\n: invalid : yaml ::: [\n?>\n<?/mock?>\n"
 	f := newTestFile(t, "test.md", src)

internal/archetype/gensection/parse.go

@@ -77,6 +77,10 @@ func FindMarkerPairs(
 					piLine := f.LineOfOffset(pi.Lines().At(0).Start)
 					diags = append(diags, MakeDiag(ruleID, ruleName, f.Path, piLine,
 						fmt.Sprintf("generated section end marker <?%s is missing closing ?>", pi.Name)))
+				} else if !isEndMarkerAloneOnLine(pi, f) {
+					piLine := f.LineOfOffset(pi.Lines().At(0).Start)
+					diags = append(diags, MakeDiag(ruleID, ruleName, f.Path, piLine,
+						"generated section end marker must be the only content on its line"))
 				} else {
 					// Well-formed nested end marker — reduce depth.
 					depth--
@@ -138,12 +142,7 @@ func handleEndMarker(
 				fmt.Sprintf("generated section end marker <?%s is missing closing ?>", pi.Name)))
 	}
 
-	// End marker must be the only content on its line.
-	seg := pi.Lines().At(0)
-	raw := string(seg.Value(f.Source))
-	trimmed := strings.TrimSpace(raw)
-	expected := fmt.Sprintf("<?%s?>", pi.Name)
-	if trimmed != expected {
+	if !isEndMarkerAloneOnLine(pi, f) {
 		return current, pairs, append(diags,
 			MakeDiag(ruleID, ruleName, f.Path, piLine,
 				"generated section end marker must be the only content on its line"))
@@ -154,6 +153,16 @@ func handleEndMarker(
 	return nil, append(pairs, *current), diags
 }
 
+// isEndMarkerAloneOnLine checks that the end marker PI is the only
+// content on its source line.
+func isEndMarkerAloneOnLine(pi *lint.ProcessingInstruction, f *lint.File) bool {
+	seg := pi.Lines().At(0)
+	raw := string(seg.Value(f.Source))
+	trimmed := strings.TrimSpace(raw)
+	expected := fmt.Sprintf("<?%s?>", pi.Name)
+	return trimmed == expected
+}
+
 // extractYAMLBody returns the YAML content from a PI's Lines(),
 // skipping the first line (the <?name line).
 func extractYAMLBody(pi *lint.ProcessingInstruction, source []byte) string {

internal/rules/include/rule_test.go

@@ -656,6 +656,28 @@ func TestFix_RecursiveExpansionWithFrontmatter(t *testing.T) {
 		"Fix output mismatch\ngot:\n%s\nwant:\n%s", got, want)
 }
 
+func TestFix_RecursiveExpansionSubdir(t *testing.T) {
+	// B is in a subdirectory and includes C relative to itself.
+	// Recursive expansion must resolve C correctly via readFS,
+	// not double the subdirectory path.
+	fsys := fstest.MapFS{
+		"sub/b.md": {Data: []byte(
+			"# B\n\n<?include\nfile: c.md\n?>\n" +
+				"stale\n<?/include?>\n")},
+		"sub/c.md": {Data: []byte("Fresh from C\n")},
+	}
+	src := "# A\n\n<?include\nfile: sub/b.md\n?>\n" +
+		"old\n<?/include?>\n"
+	f := newTestFile(t, "a.md", src, fsys)
+	r := &Rule{}
+	got := string(r.Fix(f))
+	want := "# A\n\n<?include\nfile: sub/b.md\n?>\n" +
+		"# B\n\n<?include\nfile: c.md\n?>\n" +
+		"Fresh from C\n<?/include?>\n<?/include?>\n"
+	assert.Equal(t, want, got,
+		"Fix output mismatch\ngot:\n%s\nwant:\n%s", got, want)
+}
+
 // =====================================================================
 // No FS
 // =====================================================================