No longer invoke scripts using `bash` or `source`

This allows the bash arguments at the top of each script to be
respected.

fix bug 1063104
Make non-executable scripts executable.

fix bug 1063104
Merge pull request #2335 from bramwelt/fix-bug-1063104-directly-invoke-scripts

fix bug 1063104 - Directly invoke bash scripts in Makefile and build.sh
Clean `build`, not `builds`, directory.

fix bug 1062710
Change build directory from `builds` to `build`

fix bug 1063155