When working with submodules and submodule modifies some tracked files during build,
the consecutive builds will file on submodule update, with a git error of unstaged changes.

Although build should not change tracked files it could happen due to programmer mistake.

One can bypass it with
git submodule foreach git checkout %sha1%
as a first build step

Note that git clean is not an option for builds that uses bower or npm, since they download packages from web, and generally work very long.