Remove symlinking node_modules workaround
  Remove top-level Gruntfile and grunt-shell dependency

Implement workaround from https://github.com/gruntjs/grunt-contrib-watch/issues/162
with grunt.file.setBase in order to run grunt (and watch) on a
per-problem basis

Update bootstrap script to utilize new workaround in generated
Gruntfiles

Still not ideal, but much better than the previous workaround