Leave stone superstructures intact for they are allowed! Leave the hand-span elevation for it is allowed, together with the two grave-posts! It is established that the Prophet ﷺ placed a rock on top of `Uthman ibn Maz`un's grave - Allah be well-pleased with him - saying: "With it I shall designate the grave of my [milk-]brother and later bury in it whoever dies among my relatives."2 Kharija ibn Zayd said: "I can see myself when we were young men in the time of `Uthman [ibn `Affan] - Allah be well-pleased with him. The strongest one of us in high jump was he who could jump over the grave of `Uthman ibn Maz`un and clear it."3
1 The grave of Amina bint Wahb the Prophet's mother ﷺ .
2 Narrated from an unnamed Companion by Abu Dawud and al-Bayhaqi in al-Kubra (3:412) with fair chains cf. Ibn Hajar, Talkhis al-Habir (2:134); Ibn al-Mulaqqin, Tuhfat al-Muhtaj (2:29). The complete report states that the Prophet ﷺ asked a man to place a rock on top of Ibn Maz`un's grave; when he was unable to move it, he - Allah bless and greet him - rolled up his sleeves and helped him and the whiteness of his arms was visible. Ibn Maz`un was the first of the Muhâjirûn buried in Baqi` al-Gharqad. Ibrahim, the Prophet's son, was buried next to him.
3 Cited by al-Bukhari without chain in his Sahih chapter-title, "[Placing] a Stalk on Top of the Grave." Ibn Hajar said in Fath al-Bari (3:256=1959 ed. 3:223): "Al-Bukhari narrated it with its [sound] chain in al-Tarikh al-Saghir (1:42)... It contains a proof for the licitness of raising high the grave and elevating it above the surface of the earth."
Ironically, when the Sufi cemetary was razed to make way for the university of Damascus and its campus in that city, King `Abd al-`Aziz ibn Sa`ud intervened personally to preserve intact the tombs of Ibn Taymiyya and his student Ibn Kathir.
As for the report on the qubba (= khayma, fustat, i.e. a tent) built for one full year over al-Hasan ibn al-Husayn ibn `Ali's grave by his wife Fatima bint al-Husayn ibn `Ali is narrated in Ibn Abi al-Dunya's Kitab al-Qubur and cited in al-Bukhari's Sahih in mu`allaq form (chainless) but positively attributed by the Imam, i.e. he considers it sahih even if it may not necessarily meet his standard in the Sahih. Chapter titled: "The dislike over what is considered taking the grave as a place of worship." After a year she folded up the tent and heard a voice saying: "Had they but found what they had lost!" Another voice replied: "Nay, they despaired and then turned back!" Ibn Hajar said in Fath al-Bari (3:238=1959 ed. 3:200): "Admonishment came to them in the form of the two callers decrying what they had done. It seems they were from the angels or else from the believers of the Jinn. Al-Bukhari mentioned this report only because it agrees with the proofs of the Law, not because it is a proof in itself."
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