MacOS – /usr/bin/nice and Handbrake

Terminal.app correctly starting the shell does’t mean much: it runs /usr/bin/login (with the full path) by default, which invokes your default shell (again: defined with a full path) as an interactive login shell (which will in turn read both .profile and .bashrc and leave you with a working $PATH). Your problem is non-interactive shells, which do neither, do not get any $PATH settings. That seems to point to OS X’ default path settings having somehow been clobbered.

To check this, run cat /etc/paths. The output should (at the very least) be

/usr/bin
/bin
/usr/sbin
/sbin

(these are the defaults on a pristine OS X install). If the first two are missing, you have your cause – and an easy solution:

mv /etc/paths /etc/paths.old # if you want to keep the current contents
def_paths=(/usr/bin /bin /usr/sbin /sbin)
for p in ${def_paths[@]}; do echo $p >> /etc/paths; done
cat /etc/paths.old >> /etc/paths # append previous contents

Note that as /etc/paths is owned by root, you will have to sudo su for this to work.

From OS X 10.9.1: /usr/bin/codesign

Alternatively, grab it from your Recovery HD:

diskutil mount Recovery\ HD
hdiutil mount /Volumes/Recovery\ HD/com.apple.recovery.boot/BaseSystem.dmg
sudo cp /Volumes/OS\ X\ Base\ System/usr/bin/codesign /usr/bin/codesign

^{I recommend you do a permissions repair after copying.}