Fix GH-98

Store IDs of non-chunked elements.
Closes #98.

phpdotnet/phd/Index.php

@@ -383,6 +383,9 @@ public function format_chunk($open, $name, $attrs, $props) {
                 $this->chunks[] = $id;
                 $this->currentchunk = $id;
                 $this->storeInfo($name, $id, $id);
+            } else {
+                $this->storeInfo($name, $id, $this->currentchunk, false);
+                $this->appendID();
             }
             return false;
         }

phpdotnet/phd/TestIndex.php

@@ -0,0 +1,8 @@
+<?php
+namespace phpdotnet\phd;
+
+class TestIndex extends Index {
+    public function getIndexes(): array {
+        return $this->indexes;
+    }
+}

tests/index/bug_GH-98.phpt

@@ -0,0 +1,37 @@
+--TEST--
+Bug GH-98 - Non-chunked section is not linked
+--FILE--
+<?php
+namespace phpdotnet\phd;
+
+require_once __DIR__ . "/../setup.php";
+
+$xml_file = __DIR__ . "/data/bug_GH-98.xml";
+
+Config::init([
+    "index"    => true,
+    "xml_file" => $xml_file,
+]);
+
+$index = new TestIndex;
+$render = new TestRender(new Reader, new Config, null, $index);
+
+$render->run();
+
+$indexes = array_keys($index->getIndexes());
+
+echo "Indexes stored:\n";
+
+var_dump(in_array("non-chunked.element.id", $indexes));
+var_dump(in_array("another.non-chunked.element.id", $indexes));
+var_dump(in_array("chunked.element.id", $indexes));
+var_dump(in_array("another.chunked.element.id", $indexes));
+var_dump(in_array("bug-GH-98", $indexes));
+?>
+--EXPECT--
+Indexes stored:
+bool(true)
+bool(true)
+bool(true)
+bool(true)
+bool(true)

tests/index/data/bug_GH-98.xml

@@ -0,0 +1,28 @@
+<?xml version="1.0" encoding="utf-8"?>
+<chapter xml:id="bug-GH-98">
+
+ <sect1 xmlns="http://docbook.org/ns/docbook" annotations="chunk:false" xml:id="non-chunked.element.id">
+  <para>
+   Content to ensure this elements is indexed
+  </para>
+ </sect1>
+
+ <section xmlns="http://docbook.org/ns/docbook" annotations="chunk:false" xml:id="another.non-chunked.element.id">
+  <para>
+   Content to ensure this elements is indexed too
+  </para>
+ </section>
+
+ <sect1 xmlns="http://docbook.org/ns/docbook" xml:id="chunked.element.id">
+  <para>
+   Content to ensure this elements is indexed as well
+  </para>
+ </sect1>
+
+ <section xmlns="http://docbook.org/ns/docbook" xml:id="another.chunked.element.id">
+  <para>
+   Content to ensure this elements is also indexed
+  </para>
+ </section>
+
+</chapter>