"If you want to do well then you should remember that a good shinobi would not commence a covert activity until everything sits well within his mind" - Natori Masatake (Shoninki)
In-nin (dark shinobi) are the skills of creeping in the darkness or being out of the enemy's sight. This infiltration through stealth could also be done during the daytime as long as the enemy does not spot the shinobi.
The Akutagawa Kaden manual claims a shinobi must learn to imitate animal sounds during infiltration so that the people indoors would ignore any movement outside.
Both the Giyoshu military manual and the Shoninki shinobi manual advise paying attention to the shadows made by the moonlight, and taking cover in even the smallest shadow. They also mention the use of the kaginawa grappling hook and using a katana or wakizashi as a foothold when climbing. When infiltrating grilled rice would be brought along to be fed to watchdogs that bark. This would quiet them.
Giyoshu In-nin Edit
"Be effective and return with evidence"According to the Giyoshu manual, when inside, shinobi would crouch under bamboo floors following the "path of the weasels" and imitating the sound of a rat's footsteps or the sound of insects. If a shinobi met an enemy during infiltration, the manual advises not retreating without proper reason. If it's difficult to escape from the enemy, a shinobi should approach the enemy and pretend to be someone else to avoid getting killed.
As specified by the Giyoshu, when sneaking in a shinobi shouldn't carry too many tools. Food and medicine for stomach-aches should be brought along above all else. The Giyoshu grappling hook has the rope passing through bamboo tubes.
The Giyoshu also claims shinobi should observe the route ahead, and depending on how moonlit a night is , if at all, a shinobi would change his mannerisms or outfit. A shinobi should also pay attention to any footprints found. The manual also recommends infiltrating at twilight or before dawn. When infiltrating, a door could be drilled first and then a hole or an opening could be cut out. Alternatively, a shinobi could burn out a window-like hole gradually. The opening would be covered with a piece of clothing and when a shinobi decides to sneak in, he would use the hole and seal it back up.
When infiltrating, the Giyoshu manual claims that if a shinobi makes a noise due to the enemy's movements startling him, he will be caught. A shinobi should not exit from the same route before dawn as people sleep lightly and are easily awoken. A shinobi should also return with evidence of him completing the mission.
When infiltrating while wearing armor a shinobi should tie a yonshaku-tenugui around the thighs like an outer sash so the armor won't rattle.
"Be aware that "stealing in" should no be done at all in haste and never without enough care taken, lest you may fail" - Natori Masatake (Shoninki)According to Natori Masatake, author of the Shoninki manual, if a shinobi comes across a person and doesn't want to be seen he should cover his face with his hand in order to conceal it in the moonlight. Natori then goes on to state that there is no best time to infiltrate but a shinobi should aim for a time when the inhabitants of a house are busy the most.
The best times to infiltrate under the cover of night are around dusk; the hours of the Boar (亥) (9 - 11 PM), the Rat (子) (11 PM - 1 AM) and the hour of the Tiger (寅) (4:20 - 5 AM). Or when horizontal clouds appear over the peaks of the mountains because dawn is approaching.
During daytime, the best times to infiltrate are the hours of the Hare (卯) (5 - 7 AM), of the Horse (午) (11 AM - 1 PM), and of the Rooster (酉) (5 - 7 PM).
If the shinobi doesn't know what time it is he would simply check to see which nostril he's breathing through, if it's his left, the time would be an even number, if it's the right, it would be an odd number. Another way of telling the time would be through a cat's eyes. The closer to midday it is the narrower the pupils would be. The same could be done with human eyes.
Most people would go to bed no later than the hours of the Boar (9 - 11 PM) and are asleep in the first third hour of the Ox (1 - 1:40 AM) and wake in the first third of the Rabbit (5 - 5:40 AM). If someone is truly asleep his breathing would be irregular and he would move slightly every two hours.
Natori alludes to good hiding places such as old wells, behind large stones or trees, cliffs, mountains, caves, toilets, sticking close to walls or, alternatively, using yo-nin to hide in plain sight. A shinobi should always check to see if there are any bodies of water or animals near by as they can alert guards to the shinobi's presence. Bodies of water create ripples and birds fly away to avoid people. This can be seen even at night.
He then recounts the technique of dangling a small stone at the end of a thread and hanging it at 15 or 18 mm above the ground in the morning. When the master of the house falls asleep the stone will touch the floor. When walking on a roof a shinobi should climb up from an area around the beams and walk along the ridge. If there is something strange in his way he should throw a stone up on the roof first to see what it is in case his eyes are playing tricks on him. Natori then mentions ryō'ori (両おり) the skill of avoiding capture on a roof. A shinobi would drop a stone one way while going down the side of the house in the opposite direction. This would confuse the enemy.
On dark moonless nights a shinobi could imitate dogs to avoid being seen. He could dig holes beneath walls and hedges to destroy them, growl when passing under hedges, sleeping, stretching or when facing down other animals. They sometimes tremble when they growl, which could be mimicked by shaking the edge of one's kimono, and bark when threatening people. When walking along a road, a dog would walk alongside a hedge or fence. The skill of imitating cats is mentioned in the Shoninki although Natori claims the skill is less important and less useful than impersonating dogs.
Natori then goes on to recount a technique called ai'inu (合い犬) in which a shinobi brings along a bitch to mate with an aggressive male guard dog. This will occupy the male watchdog. A more common technique is feeding the dog grilled rice repeatedly beforehand to befriend him. If a shinobi adds some residue of the sesame seed after the sesame oil has been extracted the rice will prevent the dog from barking. Another way of dealing with guard dogs would be feeding them machin (まちん), a poison derived from strychnine tree seeds, which will intoxicate the dogs and dehydrate them to death. Although water will cure their dehydration immediately. To counter this shinobi added iron filings to the dogs' source of water to kill them.
Nighttime isn't always the best time for a covert activity. A shinobi should use his own judgement and examine the place, time and situation. Windows that are open all night always have shutters on the other side, while windows that are closed all night don't. Windows without shutters could be easily sawed through to get to the lock and unlock it. A shinobi would saw a hole large enough to fit his hand inside, and unlock it from the inside.