It clearly outlaws the harming of civilians period

Here are quotes from Protocol 1
Additional to the Geneva Conventions, 1977
[link|http://deoxy.org/wc/wc-proto.htm|http://deoxy.org/wc/wc-proto.htm]
PART IV: CIVILIAN POPULATION
"Article 48: Basic Rule
In order to ensure respect for and protection of the civilian population and civilian objects, the Parties to the conflict shall at all times distinguish between the civilian population and combatants and between civilian objects and military objectives and accordingly shall direct their operations only against military objectives."

Article 49: Definition of Attacks and Scope of Application
"Attacks" means acts of violence against the adversary, whether in offense or in defense.
The provisions of this Protocol with respect to attacks apply to all attacks in whatever territory conducted, including the national territory belonging to a Party to the conflict but under the control of an adverse Party.
The provisions of this Section apply to any land, air or sea warfare which may affect the civilian population, individual civilians or civilian objects on land. They further apply to all attacks from the sea or from the air against objectives on land but do not otherwise affect the rules of international law applicable in armed conflict at sea or in the air.

Article 50: Definition of Civilians and Civilian Population
A civilian is any person who does not belong to one of the categories of persons referred to in Article 4 A 111, lIl, (31 and 161 of the Third Convention and in Article 43 of this Protocol. In case of doubt whether a person is a civilian, that person shall be considered to be a civilian.
The civilian population comprises all persons who are civilians.
The presence within the civilian population of individuals who do not come within the definition of civilians does not deprive the population of its civilian character.

Indiscriminate attacks are prohibited. Indiscriminate attacks are:
those which are not directed at a specific military objective;
those which employ a method or means of combat which cannot be directed at a specific military objective; or
those which employ a method or means of combat the effects of which cannot be limited as required by this Protocol; and consequently, in each such case, are of a nature to strike military objectives and civilians or civilian objects without distinction.
Among others, the following types of attacks are to be considered as indiscriminate:
an attack by bombardment by any methods or means which treats as a single military objective a number of clearly separated and distinct military objectives located in a city, town, village or other area containing a similar concentration of civilians or civilian objects; and
an attack which may be expected to cause incidental loss of civilian life, injury to civilians, damage to civilian objects, or a combination thereof, which would be excessive in relation to the concrete and direct military advantage anticipated.

I have already pointed out here that the settlemennts do not violate the Geneva Convention (see the comments I posted from Eugene Rostow). Israel has tried very hard not to kill innocent civilians, it has used precision weaponry etc. to minimize the casualties.

You said that dropping a nuclear bomb and killing civilians is not a war crime. I pointed you to the Geneva Convention which clearly states that indiscriminate attacks where civilians are likely to be killed are prohibited. This clearly disallows the above.