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As you can see here most/all of them are wearing life-jackets, and that's normally something you wouldn't wear all the time on a boat so I would guess that they put them on as protection preparing to attack the Israeli soldiers.
Edit: on this video you can see several activitst wearing gas-masks as well life-jackets for protection, so they seemed to be preparing for violent confrontations.......
On the first video the crowd seems to stop when at least one of the soldiers seems to draw a sidearm, rubber-bullets seems to have been used first without effect.
A couple of reports I've seen says that the activists on the boat took at least one gun/pistol from an Israeli soldier
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And tear-gas usually doesn't work very well when you fastrope down from a chopper (it's a tiny bit of wind below you then.
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If they startet to use such things before boarding the ship it could also escalate a situation unnecessarily, and after the first soldiers where attacked it could be even more dangerous to use it.