It means Don't use makeshift (or ready-to-use) solutions.
I have tried to find the origin of the phrase and the only explanation I have found is is here ( in the comments).
Paving the cow path is an expression I heard first in the east coast of the US. The story as it was told to me is as follows:
When the city of Boston was new and unpaved the city fathers decided against laying out a regular street plan and instead merely paved the paths that had been worn by cattle. The implication is that this has resulted in a chaotic inefficient street plan that lacks logic. The admonition not to “pave the cow path” is supposed to remind us not to enshrine a makeshift solution.
Of course there are problems with this phrase. Cattle are actually a pretty good at finding the path of least resistance, which is often the best route for a road.
The Boston story basically matches the actual source. The phrase originates with a poem written by Sam Walter Foss (1858-1911) originally of New Hampshire, but he did live in Boston for a period of time, so the reference to Boston streets may be legit. The poem was called "The Calf-Path" and can be found if searched on the Net. Somehow Calf has turned into cow, so perhaps Foss was also aware of the inherent travel efficiencies of cows, and used the meandering of calves to make his point.
The poem The Calf-Path by Sam Walter Foss.