bugfix: accurate File.digits indexes, Sequence.contains fix

File constructor
----------------

Problem: when determining the index of a digit match,
used String.indexOf() - when two matches began with the same digit
this method returns just index of the FIRST match.

Fix: use the stateful RegExp instance with a `while` loop.

Sequence.contains
-----------------

Problem: given these three files
  a123Sequence.0001.txt
  a123Sequence.0002.txt
  a124Sequence.0001.txt

Sequence.contains tests against the first file in the sequence (this
is arbitrary) - the test between `a123Sequence.0001.txt` and
`a124Sequence.0001.txt` succeeds because there is only one difference
group.

Fix: add a test to make sure that single difference group is found at
the sequence's significantGroup.index.