'Stones and trees calling out 'kill the Jews',' as revealed in the hadiths, is meant in a figurative sense. A believer will notact according to a voice coming from stones and trees and will not kill an innocent person. A Muslim acts solely according to the moral values of the Qur'an

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Abu Huraira (ra) reported Allah's Messenger (saas) as saying:
"The Last Hour would not come unless the Muslims will fight against
the Jews. The Jews would hide themselves behind a stone or a tree and
a stone or a tree would say: 'Muslim, or the servant of Allah, there
is a Jew behind me; come and kill him;' but the tree Gharqad would not
say, for it is the tree of the Jews."
(Sahih Muslim, Kitab al-Fitan wa Ashrat as-Sa'ah, Book 41, 6985)
"So that Jews will hide behind trees and the tree will say "Muslim!
The servant of Allah! Come, look there is a Jewbehind me, he hid here,
behind me, come and punish him". Only the tree Gharqad will not say,
for it is the tree of the Jews."
(Kitab al-Fitan, hadith. 2239)
One statement by Mr. Adnan Oktar concerning hadiths in which our
Prophet (saas) refers to "stones and trees in the End Times telling
Muslims the location of Jews hiding behind them and saying 'Come and
kill them'," reads:
"We look at events in thelight of the Qur'an and the hadiths. But one
cannot issue a pronouncement on the basis of one single verse in the
Qur'an. One must look at the verses as a whole. The same applies to
the hadiths. The otherhadiths complement oneanother. Therefore, if
someone comes and tellsus, 'There is a Jew here, come and kill him,'
we will not kill him. Why should we? That person would have to commit
a crime. And if he commits a crime he will have to be tried. And the
judge will pronounce sentenceat the end of the trial. There is a whole
system and legal procedure involved. It does not mean that anyone who
sees him can kill him andtry him himself. We can see what this hadith
means by looking at others. Otherwise, it is a sin to kill an innocent
Jew, a person, a child, standing there, and heed a voice from a stone
telling us to kill them. That is unacceptable. We must grasp what our
Prophet (saas) really means. It would appear the hadithmeans this:
Jews who are atheists or enemies of religion cannot hide. Those who
hide among wood or stones will be located using all kinds ofelectrical
devices and equipment, and the evil and activities of these people
will thus be prevented, and that will be a punishment for them. That
is what the hadith may be implying. (From Mr. Adnan Oktar's interview
on Adiyaman Asu TV and Kackar TV on June 3, 2010)
http://tr.harunyahya.tv/videoDetail/Product/27114/WHAT_IS_THE_EXPLANATION_OF_THE_GHARGAD_TREE_MENTIONED_IN_THE_HADITH?
Mr. Oktar interprets this clearly figurative hadith in a very wise
fashion. The content of the hadith is obviously figurative because the
verses of the Qur'an regarding killing are quite explicit. It is clear
that no decision to kill can be taken on the basis of producing a
pronouncement on the basis of a voice from stone, trees or wood. There
is no verse to that effect in the Qur'an. According to the Qur'an, a
Muslim learns from the Qur'an, not from tree or wood. Nowhere in the
Qur'an is it revealed that a tree or wood can bear witness for a
Muslim. According to the Qur'an, it is what Muslims bear witness to
that matters.
Allah compares hypocrites to "blocks of wood" in the Qur'an (Surat
al-Munafiqun, 4). Allah also compares unbelievers to rock, "your
hearts became as hard as rocks." (Surat al-Baqara, 74) A Muslim does
not behave according to rocks and wood. He acts according to what
other Muslims say.
It is incompatible with the Qur'an and unlawful for an innocent person
to be killed according to a statement issued from a stone. To say that
such a ruling can be given without trying that person would mean to
say that the voice from the stone was revelation(Surely Allah is
beyond that). It would therefore be insanity, murder, to say, "I
killed a man because of a voice from a stone" or "A rock told me, and
I killed him." A Muslim would never act in such a way toward anyone
without trying them as the law demands.
If rulings were to be extracted from rock or wood, then what the rock
or wood said wouldbe regarded as Divine revelation. Since no other
book apart from the Qur'an will come, to say such a thing would be to
claim that rock or wood would reign over us (Surely Allah is beyond
that). A Muslim acts by the light of the Qur'an and the hadiths of our
Prophet (saas), not rock and wood. If a person regards stone and wood
as issuing revelation, if he says, "what a rock says is revelation,
rock bestows revelation on me, stone and wood rule me," thenhe is
departing from the religion. Under that belief, the rock might tell
him other things, too. It will say anything and cause the person to do
other things. There are no verses in the Qur'an concerning a Muslim
obeying rock andwood.
In addition, Jews are people given protection in the time of our
Prophet (saas) and who followed Muslims. The compassion and justice
shown by the Prophet (saas) in the light of the Qur'an, acted as a
role model for subsequent Muslim rulers. Allah says in the Qur'an,
"... Do not let hatred for a people incite you into not beingjust. Be
just. That is closer to taqwa" (Surat al-Ma'ida, 8). Allah also
commands Muslims to ensure the safety even of the idolaters (pagans
who do not heed Allah's revelation): "If any of theidolaters ask you
for protection, give them protection until they have heard the words
ofAllah. Then convey them to a place where they are safe...." (Surat
at-Tawba, 6) A Muslim will therefore uphold justice, for Allah's sake,
in the face of anyone and everyone and will only seek solutions to all
matters as revealed in the Qur'an.