Improve the heuristics for "pub get" is needed.

Instead of relying only on modification times, this does a more complex
compatibility check if the modification times of the pubspec, lockfile,
and .packages file aren't ordered properly. If they are up-to-date, it
updates the modification times accordingly.

This also fixes a case where "pub run" wasn't properly checking that the
dependencies were up-to-date.

Closes #1322

R=rnystrom@google.com

Review URL: https://codereview.chromium.org//1307853004 .