What Hermione didn't know was that Harry was under his invisibility cloak and was watching her. He even heard her whisper to herself before she hurriedly starting putting books back onto their rightful places on the shelves.
As the cloak was able to be folded up into a very small package, Harry kept it on his person at all times ever since he'd once caught Weasley going into his trunk and taking things.
He'd also figured out that the cloak was also the third Deathly Hallow and knew the story. As Death was unable to find the third brother until he'd removed the cloak from himself, he knew Dumbledore had to have done something to it to allow the old man to see through it; as he clearly did the night he was under it in Hagrid's cabin when Fudge and Malfoy turned up to arrest the big oaf.
As soon as he'd figured that out, and after binding Dobby to himself, he'd had the elf inspect it. Dobby had found a few charms on it anchored to new stitching.
Having the little elf unravel the stitching, Harry had taken to carrying that thread around, so the old man would not know it had been discovered.
Once he'd discovered, or Dobby had discovered, that particular tracker-come-beacon, he had the little elf scan the rest of his property. And what a veritable panoply of charms the little elf found. Mail redirection, anti-scry, listening, confounding and anti-muggle notice-me-not jinxes; trackers; beacons; blood-based magics and others even Dobby did not recognise. After having Dobby muffle the listening charms, Harry then explained what he needed the elf to do.
Everything, except the anti-scry charm, was removed from Harry's personal property and transferred to a few inanimate objects Harry had then taken to carrying about on himself. He'd already figured out that, if he appeared to be free of them, the Headmaster would both want to try and figure out why and replace them. However, moving them to inanimate objects, meant he was able to leave them behind when he wanted to accomplish something without the old man knowing he had 'slipped his leash'.
One of those occasions was when Harry visited the goblins between second and third year. He'd left those objects back in his room in the Leaky Cauldron to ensure Dumbledore thought he'd not been in to see them.
Now he'd done the 'Big Reveal', as he called it, he'd watched Hermione head for the library and, while she was otherwise busy, headed out to the lake edge and banished those objects as far out into the water as he could. The only one he'd retained was the anti-scry ward; as Dobby had assured him it stopped everyone, including Dumbledore, from scrying his location. He wondered if the old man had stopped to think if it would or not.
It wasn't until a few moments after tossing them into the lake he realised he should have kept them and handed them over to Madam Bones. They were, after all, evidence of one of the 'crimes' of which he believed the old man guilty.
'Oh, well,' he had thought to himself with a mental sigh. 'She has more than enough to convict the old bastard, as it is.'
Now he watched as Hermione, his real best friend, discovered he was right and began to pack up. Knowing she would immediately seek him out, he beat a hasty but silent retreat back to the Gryffindor common room. He also knew the aurors would have already figured out he hadn't gone for a 'lie down' as he'd told them and were currently scouring the castle looking for him. He needed to get back to the common room and give them time to tell him off for disappearing on them before Hermione returned.
Making it back to the common room, and getting told off by the aurors as he thought he would, it was less than ten seconds later that Hermione entered and, as soon as she saw him on 'their' couch, headed to join him. Sitting down she only glanced at him before averting her eyes downward and saying, "Sorry, Harry."
"Alright," he said. "What are you sorry for?" "You were right about the house elves. They're not slaves," she quietly replied.
"Uh-huh," he quietly agreed.
"No 'I told you so's?" she asked. "Nope," he replied. "No need." She seemed to think for a long few moments before she almost plaintively asked, "Have I always been that bad?" "Yes," he immediately replied. When she winced he added, "You have this bad habit of accepting things as fact based on what you know from the muggle world. The magical world is not the muggle world, Hermione. There are many things in the wizarding world that have no contemporary in the muggle world. The issue of house elves and how they're symbiotic creatures is just one of those."
"But, it just seems so wrong!" she practically whined.
"It would be, if it weren't for the need of house elves to bond to stay alive," he said. "Plus, you also need to stop thinking of house elves as people. They're not."
"They might not be human, Harry," she argued; "But they are people. They're just a different sort of people to humans."
"Yes; different," he shot back. "As in not the same."
"But, they are a people," she said. "They're intelligent. They can speak. We can speak with them. They're capable of higher thought."
"And where do you draw the line regarding intelligence, Hermione?" he asked. "If not at house elves, what about: goblins, trolls, giants, centaurs, chimpanzees, bears or even dolphins? Where do you draw the line at what constitutes 'speak'?"
"I..." she stuttered, "I - don't know."
"Look," he said, trying to explain. "You were raised with wholesome Christian values in a modern British society - a modern muggle British society. In that society the next creature down on the list of intelligence is dolphins, followed by chimpanzees. And no one considers thempeople."
With a sigh he added, "This is not modern muggle British society; this is wizarding Britain. And it is effectively ruled by those whose understanding of muggle British Society is what they've seen out the front windows of the Leaky Cauldron, or what they've seen at Kings Cross Station, or what they've seen out the windows of the Hogwarts Express. Even then there are a great many who've not even seen that.
"Wizarding Britain, as a society, is closer to... say... Iran. Except, instead of it being a theocracy, as it is there, it's a... magi-ocracy. At least, that's the closest I could come to as an example. Those who have had magic in their families the longest, rule. Understand?"
Though she looked almost stunned at Harry's explanation, she replied, "Errr... yes; I think so."
"Good," he firmly stated with a short nod of his head. "Because, your oft-times negative attitude to certain 'traditions' of the magical world offends those raised in this world. And, it's not that they don't know any better, either. It's that they detest someone, like you, coming into their world and trying to force them to change. That attitude is no different than Muslims coming to Britain and trying to force everyone to start obeying Sharia law."
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