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I can create symlink (something like that) and it works. Until next restart. How do I force iterm to restore symlinks? How do I preserve these after a system update?

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You must be very confused. The symlink is part of the filesystem and has nothing to do with iterm. If your symlinks are going away, it is for another reason. Where (which folder) are you putting these symlinks? – Kevin Panko Oct 25 '13 at 18:43
I'm putting them in /bin – Agzam Oct 25 '13 at 19:08
might be they were gone after I updated to Mavericks? – Agzam Oct 25 '13 at 19:09
up vote 2 down vote accepted

Since you stated you just updated to Mavericks… that's the culprit. Doing an OS upgrade (or a reinstall of OS X) will overwrite system directories, /bin being one of these.

If you don't want your links changed, it's better to put them somewhere the OS will not overwrite, such as /usr/local/bin. You need to add this directory to your PATH though.

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