Shift all DependencyNodes indexes -1 in ClearParser.

For "Michael ran down the hill."

Before:
```
Michael 0 NNP
ran 8 VBD
down 12 IN
the 17 DT
hill 21 NN
. 25 .

nsubj(ran-3, Michael-2)
root(ROOT-0, ran-3)
prep(ran-3, down-4)
det(hill-6, the-5)
pobj(down-4, hill-6)
```

After:
```
Michael 0 NNP
ran 8 VBD
down 12 IN
the 17 DT
hill 21 NN
. 25 .

nsubj(ran-2, Michael-1)
root(ROOT-0, ran-2)
prep(ran-2, down-3)
det(hill-5, the-4)
pobj(down-3, hill-5)
```