I dunno about checking in the build directory. Having a working version of the build in the repo isn't necessary when your dependency versions are locked in shinkwrap.json. Therefore your build is completely reproducible. As for eliminating extensive tooling on your prod server, I believe a common practice is to build on your dev laptop and rsync the build directory to the server.
Do you ever run into merge conflicts in the build directory?
> Do you ever run into merge conflicts in the build directory?
Those files should always be rebuilt fresh before committing. Just quickly do whatever to clear it from the conflict queue -- probably some version of "take mine" or "take theirs". Merge the actual source files as necessary, then rebuild. Commit and just blindly clobber whatever existed in the build directory, because you just rebuilt it and you know it's the correct version.
Do you ever run into merge conflicts in the build directory?