If there are symlinks and you followed them, I think that you cannot know how you reached a file; You can test yourself:

mkdir -p real/subdir
ln -s real link
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#!/usr/bin/perl

use Cwd;

for $dir ('real/subdir', '../link/subdir') {
        print "changing to $dir\n";
        chdir $dir;
        where();
}

exit;

sub where {
        print "pwd    : ", `pwd`;
        print "cwd    : ", Cwd::cwd, "\n";
        print "getcwd : ", Cwd::getcwd, "\n";
        print "fastcwd: ", Cwd::fastcwd, "\n";
}
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This is true for Linux, I don't know for other file systems. Software like Midnight Commander or Bash shell keep track of the followed path to solve this problem.

Ciao, Valerio