one thing to remember is the Qalandia checkpoint is a very new installation so the fact that not long ago a person could travel from A to B freely. now if you live in A, you can no longer travel to B unless you have a permit (which will never be issued).
additionally whenever a palestinian gets arrested or detained (most often with an erroneous charge) they have to travel to jerusalem to appear before the judge... however as you can now see going to jerusalem is very very difficult and will soon be off limits. the soldiers who man these checkpoints do not care about anything. they are soldiers and the obey orders so if someone says "i need to appear before a judge or they will demolish my home" the soldiers at the checkpoint dont care and wont let anyone through.
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On Saturday March 25 Israeli military placed a notice at the Kalandia checkpoint announcing that from March 27, 2006 only holders of a permit to enter Israel will be allowed to cross the checkpoint to the West Bank village of Al Ramm.
By restricting Palestinian access in this way, the Israelis have effectively annexed the village minus its West Bank residents to Israel. cutting it off from the rest of the West Bank. The restriction will also cement the illegal annexation of occupied East Jerusalem.
The Kalandia checkpoint is flanked on both sides by the annexation Wall. Olmert’s Kadima party has admitted that the Wall is not a temporary security measure as Israel originally claimed but will be Israel’s “permanent border”.
http://www.palsolidarity.org/main/2006/03/26/notice-at-kalandia-checkpoint-al-ram-is-now-israel/