Fixed math errors in CalculateUMatrix

Refs #9749
Fix first few algorithm problems.

Refs #9749
Fix code directive errors.

The correct directive is 'code-block' and python should have a lower case
p.
Refs #9749
Fix more sphinx errors.

Refs #9749
Fix for earlier version of docutils.

The code role was introduced in 0.9 but a lot of places still use 0.8
Refs #9749
Fix a few more docs errors.

Refs #9749
Fix more docs sphinx errors.

Refs #9749
Fix more sphinx warnings.

Refs #9749
Remove an unused connection.

Refs #9749
Remove cout statement

Refs #9749
Merge remote-tracking branch 'origin/bugfix/9749_fix_remaining_sphinx_errors'