In computer science terminology, a backdoor is a way to access a computer system that is hidden from casual inspection of the system. Although backdoors are hidden, they are always coded on purpose. A backdoor may only be known in secret by a single rebel programmer in a software company. A virus can also be classified as a backdoor virus if the virus grants remote users access to your computer that you do not know about.
After Neo passes Seraph's test by fighting with him, Seraph takes Neo into backdoors of the Matrix. We get immediate confirmation that these backdoors are indeed "hidden from casual inspection of the system," because Link loses track of where Neo is while Neo is in the backdoors. We also see that the backdoors have at least one considerable purpose within the system, namely to provide additional security to ensure that only the One can reach the Source. So, this backdoor program in the Matrix is not a virus, nor is it secretly known by only one or two programs. Obviously, even the Architect knows about backdoors since Neo cannot reach the Source without them. But they are certainly hidden from bluepills in the Matrix and redpills/hackers outside the Matrix.
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