fixed bug when running clean on a already clean directory
Removing "as.matrix" from caliper examples.

The calls to match_on and caliper were wrapped through as.matrix, "for convenient presentation only".  But on my machine I couldn't see any difference between what that produced and what I got without the as.matrix. So I'm assuming that this is a relic of some earlier version of the print methods for ISMs, and taking out the as.matrix'es. Do revert if I am mistaken.
Adding examples of calipers on a manifest variable
Edited docs for match_on formula method

I noticed that the documentation for match_on's formula method didn't disambiguate squared and unsquared Mahalanobis, so I did that, in the process adding more detail otherwise as well.
Adjustments to match_on formula method docs

Edited details of the formula method help page. Inserted a URL pointing to the "How to write your own compute method" wiki page on the optmatch github site.
No devtools development dependency

We used devtools exclusively to download an unreleased version of
roxygen2. Since devtools does not easily install on R < 3.0, it was
easier to just fetch the package manually.
Merge branch 'master' of github.com:markmfredrickson/optmatch
Merge branch 'master' into issue-44
tests show that addition on re-ordered matrices fail