"designed to increase programmer productivity as well as reducing ...": "reducing" should be "to reduce"; the two items here require the same form as they both follow from "designed to".
"As well as" is used with closely related items plus an additional item that requires different phrasing, eg, "He wanted to look smart and successful, as well as get Jenny's attention."
This is technically wrong: "He wanted to look smart, successful, and get Jenny's attention" (although you may see it used informally).
"The new software was designed to increase programmer productivity and reduce the company's total invested cost" is best, although I believe you could quite correctly say
"The new software was designed to increase programmer productivity, as well as to reduce the company's total invested cost..."
Here you are giving more emphasis to the first item: increasing productivity is the priority, but reducing cost is also a goal.