How do I get a fully qualified path in Matlab/Octave?

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You can use this one line function (tested only on Unix like systems):

function pathOut = fullpath(pathIn)
[status pathOut] = system(sprintf('TEMP=$PWD; cd "%s"; echo $PWD; cd $TEMP;', pathIn)); 
return

For example, suppose that the current directory is /Users/zuliani/Documents/Temp. Then:

octave:1> fullpath('.')
ans = /Users/zuliani/Documents/Temp
octave:2> fullpath('../../Documents/')
ans = /Users/zuliani/Documents