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Improve fill in various ways

Christoph Groth requested to merge cwg/kwant:fill into master

This started after I wrote closest() and wanted to make fill()'s start accept only sites. In the end fill got rewritten twice, but the result should be more correct and consistent. It's also faster: the old fill was 3-4 times slower than shape(), the new fill is just 10% slower.

Closes #106 (closed)

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