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```
$input_dir =~ s{^\.\./}{/};
```

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use File::Spec::Functions qw/splitdir updir catdir/;
my @input_dir = splitdir $input_dir;
shift @input_dir if $input_dir[0] eq updir;
$input_dir = catdir(@input_dir);
# $input_dir is now "set/projects/all/files"