Muhammad orders stoning

In the most canonical hadith collection, Sahih al-Bukhari:
Volume 8, Book 82, Number 805:

Narrated Jabir bin Abdullah Al-Ansari:
A man from the tribe of Bani Aslam came to Allah's Apostle and informed him that he had committed illegal sexual intercourse and bore witness four times against himself. Allah's Apostle [Muhammad] ordered him to be stoned to death as he was a married Person.

Volume 8, Book 82, Number 809:
Narrated Ibn 'Umar:
A Jew and a Jewess were brought to Allah's Apostle on a charge of committing an illegal sexual intercourse. The Prophet asked them. "What is the legal punishment (for this sin) in your Book (Torah)?" They replied, "Our priests have innovated the punishment of blackening the faces with charcoal and Tajbiya." 'Abdullah bin Salam said, "O Allah's Apostle, tell them to bring the Torah." The Torah was brought, and then one of the Jews put his hand over the Divine Verse of the Rajam (stoning to death) and started reading what preceded and what followed it. On that, Ibn Salam said to the Jew, "Lift up your hand." Behold! The Divine Verse of the Rajam was under his hand. So Allah's Apostle [Muhammad] ordered that the two (sinners) be stoned to death, and so they were stoned. Ibn 'Umar added: So both of them were stoned at the Balat and I saw the Jew sheltering the Jewess.

Volume 8, Book 82, Number 813:
Narrated Ibn 'Abbas:
When Ma'iz bin Malik came to the Prophet (in order to confess), the Prophet said to him, "Probably you have only kissed (the lady), or winked, or looked at her?" He said, "No, O Allah's Apostle!" The Prophet said, using no euphemism, "Did you have sexual intercourse with her?" The narrator added: At that, (i.e. after his confession) the Prophet [Muhammad] ordered that he be stoned (to death).

Volume 8, Book 82, Number 815:
Narrated Abu Huraira and Zaid bin Khalid:
While we were with the Prophet [Muhammad], a man stood up and said (to the Prophet), "I beseech you by Allah, that you should judge us according to Allah's Laws." Then the man's opponent who was wiser than him, got up saying (to Allah's Apostle) "Judge us according to Allah's Law and kindly allow me (to speak)." The Prophet said, "'Speak." He said, "My son was a laborer working for this man and he committed an illegal sexual intercourse with his wife, and I gave one-hundred sheep and a slave as a ransom for my son's sin. Then I asked a learned man about this case and he informed me that my son should receive one hundred lashes and be exiled for one year, and the man's wife should be stoned to death." The Prophet [Muhammad] said, "By Him in Whose Hand my soul is, I will judge you according to the Laws of Allah. Your one-hundred sheep and the slave are to be returned to you, and your son has to receive one-hundred lashes and be exiled for one year. O Unais! Go to the wife of this man, and if she confesses, then stone her to death." Unais went to her and she confessed. He then stoned her to death.

Volume 8, Book 82, Number 817:
[brief excerpt from a long hadith] Narrated Ibn Abbas:
...Allah sent Muhammad with the Truth and revealed the Holy Book to him, and among what Allah revealed, was the Verse of the Rajam (the stoning of married person (male & female) who commits illegal sexual intercourse, and we did recite this Verse and understood and memorized it. Allah's Apostle [Muhammad] did carry out the punishment of stoning and so did we after him. I am afraid that after a long time has passed, somebody will say, 'By Allah, we do not find the Verse of the Rajam in Allah's Book,' and thus they will go astray by leaving an obligation which Allah has revealed. And the punishment of the Rajam is to be inflicted to any married person (male & female), who commits illegal sexual intercourse, if the required evidence is available or there is conception or confession...
In the Qur'an "Allah" says at least 25 times that Muhammad is to be obeyed. That is one reason why most Muslim scholars accept the Bukhari hadiths and a few other hadith collections as authoritative for Muslims: canonical hadiths show what Muhammad did and said, permitted and forbade.

Also, in the earliest Muslim biography of Muhammad, on page 684 (1014-1015 in the Arabic), second caliph Umar, a companion of Muhammad, said:
God sent Muhammad and sent down the scripture to him. Part of what he sent down was the passage on stoning; we read it, we were taught it, and we heeded it. The apostle [Muhammad] stoned (adulterers) and we stoned them after him. I fear that in time to come men will say that they find no mention of stoning in God's book [the Quran] and thereby go astray by neglecting an ordinance which God has sent down.