The VLFeat reference documentation has three parts:

MATLAB functions

The reference documentation of VLFeat MATLAB commands (this is an on-line version of the documentation built in the command themsevles).

C API reference

This documentation includes descriptions of all the algorithms and hence it is useful even if you do not plan to use the C library directly.

Man pages

The documentation of the command line utilities bundled with VLFeat (this is an on-line version of the Unix man found in the src/ subdirectory.

In addition to the documentation, there are also tutorials which introduce many of the algorithms contained in the library.