Delete duplicate d3 library (#1876)

We currently use D3 in multiple locations, and have two copies of D3 v3
in our codebase. One of them is sourced from npm, while the other is
simply a minified file which is checked into Git. The latter file is
only used on the subproject dependency graph page, and the page
functions as expected with the default D3 we source from npm. This PR
deletes the duplicate copy of D3.