`jake baseline-accept` does not update project,transpile baselines

[aozgaa]

TypeScript Version: 2.1.1 / nightly (2.2.0-dev.201xxxxx)

Repro

git checkout 7b58be779b8dbf8bbf6d7f28cfcc4444ccee08b6
jake runtests-parallel
jake baseline-accept
jake runtests-parallel

Observe that the baselines for project, transpile are not updated by jake baseline-accept.

To see the changes needed to correctly update the baselines, run

git diff 7b58be779b8dbf8bbf6d7f28cfcc4444ccee08b6  b0d916bd994f667ab6b6c3c9c885da3a161f490f

[mhegazy]

Should be fixd now.