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Automated testing

I have a software that does not yet input or output anything. It currently relies on stubs, that set values to simulate inputs, or set global variables to simulate outputs.
Once the logic is OK, the technical stuff will be added.
I would now like to automate testing in the following way :
- the input stubs read data from a file
- the output stubs write data to a file
In each development stage, it would then be possible to check if the output files remain unchanged for the same set of input data.
But working with files seems impossible, and the use of the LOG command depends on the setting of breakpoints, which are impossible to keep in a consistent state over the life of the software, and also cannot be checked for differences using SourceSafe.
Would somebody be able to give me a hint of how I could do something similar to what I would like to achieve ?
Thanks in advance for any help offered.