1. A computer system comprising: a file system configured to store electronic files; a plurality of file system scanning agents configured to access the electronic files, the file system scanning agents comprising computer hardware with one or more processors and configured to compile, based on the electronic files, index data usable for classifying the electronic files, and transmit the index data over a network to be stored in one or more indexes stored separately from the file system; and a file classification server configured to, without directly accessing the content of the electronic files, access the index data previously compiled by the plurality of file system scanning agents from the one or more indexes stored separately from the file system, and classify the electronic files based on the index data, wherein classifying the electronic files comprises assigning one or more labels to the electronic files based at least in part on a set of user-defined rules and the index data previously compiled by the plurality of file system scanning agents, and wherein the file classification server is further configured to determine a probability that one or more of the electronic files should be classified as members of a category, determine that the probability is within a threshold amount from a probability threshold for classifying the one or more of the electronic files as the members of the category, and mark the one or more of the electronic files as being questionable members of the category.