Bugfix: The bootstrap.sh script isn't loading build_libraries setting properly.

Bugfix: The bootstrap.sh script isn't loading build_libraries setting properly.

The variable for the `build_libraries` setting is just `libraries`.
The code is incorrectly saving that setting in `build_libraries` variable.
Make the code save values in `libraries` variable instead of `build_variables` variable.

Add an additional conditional logic check for when setting a variable "has" key to `no`.
If the value already exists and has a `yes` assigned, then do not set it to `no`!

Do some code cleanup up:
  - Move all of the keys into a single location for the loops (one location for single values and one location for multi values).
    - Make these read only local variables.
  - Add additional safety checks for when `${key}` might be NULL.