39. Parties to the conflict shall at all times distinguish between civilians or other protected persons and combatants and between civilian or exempt objects and military objectives.
41. Attacks shall be limited strictly to military objectives. Merchant vessels and civil aircraft are civilian objects unless they are military objectives in accordance with the principles and rules set forth in this document.
See Section II Methods of Warfare section.
42. In addition to any specific prohibitions binding upon the parties to a conflict, it is forbidden to employ methods or means of warfare which:
(a) are of a nature to cause superfluous injury or unnecessary suffering; or
(b) are indiscriminate, in that:
(i) they are not, or cannot be, directed against a specific military objective; or
(ii) their effects cannot be limited as required by international law as reflected in this document.
Israel did this. This was the legal enforcing of a blockade, with warning given. Part of that enforcement is the allowance for the blockading party to board and inspect the vessel - and even to tow it to port to inspect it. This is quite clear.
When people start attacking the soldiers legally inspecting the vessel, they lose their status as civilians and turn into combatants. At this point the commandoes must adhere to the laws of combat - mainly distinction and proportionality.
SECTION II : PRECAUTIONS IN ATTACK
46. With respect to attacks, the following precautions shall be taken:
(a) those who plan, decide upon or execute an attack must take all feasible measures to gather information which will assist in determining whether or not objects which are not military objectives are present in an area of attack;
(b) in the light of the information available to them, those who plan, decide upon or execute an attack shall do everything feasible to ensure that attacks are limited to military objectives;
(c) they shall furthermore take all feasible precautions in the choice of methods and means in order to avoid or minimize collateral casualties or damage; and
(d) an attack shall not be launched if it may be expected to cause collateral casualties or damage which world be excessive in relation to the concrete and direct military advantage anticipated from the attack as a whole; an attack shall be cancelled or suspended as soon as it becomes apparent that the collateral casualties or damage would be excessive.
This was all done.
SECTION III : ENEMY VESSELS AND AIRCRAFT EXEMPT FROM ATTACK
Classes of vessels exempt from attack
47. The following classes of enemy vessels are exempt from attack:
(ii) vessels engaged in humanitarian missions, including vessels carrying supplies indispensable to the survival of the civilian population, and vessels engaged in relief actions and rescue operations;
The flotilla organizers themselves admit that their primary goal was not humanitarian but political. Their supplies were clearly not indispensable, as we have seen. No one has starved in Gaza.
(UPDATE): More importantly, the person quoting paragraph 47 ignored paragraph 48 which explicitly excludes 47 even if the aid was legitimate: (h/t anarchofascist)
Conditions of exemption
48. Vessels listed in paragraph 47 are exempt from attack only if they:
(a) are innocently employed in their normal role;
(b) submit to identification and inspection when required; and
(c) do not intentionally hamper the movement of combatants and obey orders to stop or move out of the way when required.
How much more explicit could San Remo be that Israel was allowed to stop and inspect the ship - and that the "peace activists" had zero right to resist?
SECTION V : NEUTRAL MERCHANT VESSELS AND CIVIL AIRCRAFT
Neutral merchant vessels
67. Merchant vessels flying the flag of neutral States may not be attacked unless they:
(a) are believed on reasonable grounds to be carrying contraband or breaching a blockade, and after prior warning they intentionally and clearly refuse to stop, or intentionally and clearly resist visit, search or capture;
This is pretty clear!
69. The mere fact that a neutral merchant vessel is armed provides no grounds for attacking it.
Agreed - it was that they were breaking a legal blockade.
SECTION II : METHODS OF WARFARE
Blockade
Let's quote the entire relevant blockade section, not just a part of it. The quoted text was very misleading, especially the end of paragraph 103. I am italicizing the quoted part by Israel's detractors so you can see their deception:
Section II : Methods of warfareThis is the essential section that describes Israel's rights to search and stop the flotilla. The part that the critic left out undercuts his case completely, even if you accept the untenable position that this was an aid flotilla and that the aid was essential - both clearly not true.
Blockade
93. A blockade shall be declared and notified to all belligerents and neutral States.
94. The declaration shall specify the commencement, duration, location, and extent of the blockade and the period within which vessels of neutral States may leave the blockaded coastline.
95. A blockade must be effective. The question whether a blockade is effective is a question of fact.
96. The force maintaining the blockade may be stationed at a distance determined by military requirements.
97. A blockade may be enforced and maintained by a combination of legitimate methods and means of warfare provided this combination does not result in acts inconsistent with the rules set out in this document.
98. Merchant vessels believed on reasonable grounds to be breaching a blockade may be captured. Merchant vessels which, after prior warning, clearly resist capture may be attacked.
100. A blockade must be applied impartially to the vessels of all States.
102. The declaration or establishment of a blockade is prohibited if:
(a) it has the sole purpose of starving the civilian population or denying it other objects essential for its survival; or
(b) the damage to the civilian population is, or may be expected to be, excessive in relation to the concrete and direct military advantage anticipated from the blockade.
103. If the civilian population of the blockaded territory is inadequately provided with food and other objects essential for its survival, the blockading party must provide for free passage of such foodstuffs and other essential supplies, subject to:
(a) the right to prescribe the technical arrangements, including search, under which such passage is permitted; and
(b) the condition that the distribution of such supplies shall be made under the local supervision of a Protecting Power or a humanitarian organization which offers guarantees of impartiality, such as the International Committee of the Red Cross.
Israelis know their stuff in international law and conflicts (as sshender noted earlier) . The IDF does not make a move without a team of lawyers approving it ahead of time. In this case, just reading the San Remo doc shows that Israel was perfectly within its legal rights.