Therefore, when discussing Islam and Jihad, what must be considered most applicable are Muhammad’s final teachings and commands, especially what his last wishes and instructions were regarding Jihad and violence.
From the viewpoint of the non-Muslim world, we must know which Qur’anic passages are still in force today for the Muslim community, and which are not.
Earlier statements related to peace may or may not have been abrogated by later statements related to violence, or visa versa. We must carefully examine the context of the texts to know which Jihadic directions are acceptable and in force today.
The revered work "al-Nasikh wal-Mansukh" (The Abrogator and the Abrogated) deals in great detail with many subject matters addressed in the Qur’an wherein there appears to be some conflict or contradiction.
The book goes through every sura (chapter), pointing out in full detail every verse which has been canceled, and the verse(s) which replace it.
The author notes that out of 114 suras, there are only 43 which were not affected by this concept. As an example of the scope of abrogation in the Qur’an: there are 125 versus that call for tolerance and patience which have been canceled and replaced by sura
9:5: "Fight and slay the Pagans wherever ye find them, and seize them, beleaguer them, and lie in wait for them in every stratagem (of war)....."
and sura 5:33: "For those who do not submit to Allah their punishment is . . . execution or crucifixion, or the cutting off of hands and feet, from the opposite sides, or exile from the land".
[See: Ibn Hazm al-Andalusi, An-Nasikh wal- Mansukh, Dar al-Kotob al-'Elmeyah, birute, 1986 p.27]
Muslim activists universally fail to reveal to Westerners this major doctrine, hiding the fact that earlier conciliatory passages have been rendered null and void for over 1300 years.
When Westerners discover it on their own they complain we misinterpret such writings or misapply their impact.
Muslim promoters prefer to polish Islam's image by quoting the earlier abrogated Meccan passages that call for patience and forbearance.
Spokespersons hide or omit Medinan passages that clearly call for killing and maiming.
When hearing people explain Islam claiming the earlier more peaceful verses are dominant in Islamic philosophy, one must judge between two options; Either the presenter is completely ignorant of genuine Islamic doctrine, or he is practicing officially sanctioned Islamic deceit.
Because opinions with regard to proper conduct between believers and non-believers varies widely, the question of which Qur’anic verses are ‘alive’ and being applied today, is critical to understanding ‘Real Islam’,
and potentially to our own survival. Ibn Warraq summarizes the Muslim concept of abrogation as follows:
"Contradictions do abound in the Koran, and the early Muslims were perfectly well aware of them; indeed they devised the science of abrogation to deal with them.
It is a very convenient doctrine that, as one Christian unkindly put it, ‘fell in with that law of expediency which appears to be the salient feature in Muhammad’s prophetic career’.
According to this doctrine, certain passages of the Koran are abrogated by verses revealed afterward, with a different or contrary meaning.
This was supposedly taught by Muhammad himself,
at Sura 2, verse 105: 'Whatever verses we cancel or cause you to forget, we bring a better or its like.' …
Now we can see how useful and convenient the doctrine of abrogation is in bailing scholars out of difficulties- though, of course, it does pose problems for apologists of Islam,
since all the passages preaching tolerance are found in Meccan (i.e., early suras),
and all the passages recommending killing, decapitating and maiming, the so-called Sword Verses are Medinan (i.e., later); ‘tolerance’ has been abrogated by ‘intolerance’. For, the famous Sword verse, Sura 9, verse 5, 'Slay the idolaters wherever you find them,' is claimed to have canceled 124 verses that promote tolerance and patience." [4]
FROM ISLAM UNDRESSED by Vernon Richards Chapter 2, The Doctrine of Abrogation