There is no table of contents for most items.

/**
 *  @module doctest
 *
 *  @description This is a description of the doctest module.
 */

/**
 *  Description of first function.
 *
 *    @param a Parameter A.
 *    @param b Parameter B.
 *    @param c Parameter C.
 */
function exportedFunction1 (a, b, c) { }

/**
 *  Description of second function.
 *
 *    @param a Parameter A.
 *    @param b Parameter B.
 *    @param c Parameter C.
 */
function exportedFunction2 (a, b, c) { }

Expected: Generated documentation has either a table of contents or a list of documented functions somewhere.

Actual: Generated documentation provides no overview (in any form, other than a somewhat superfluous link to the single documented module from index.html) of the code being documented. This is in contrast to all other documentation generators, and to effective documentation in general.

Consequence: Output is only somewhat useful, especially for large bodies of code.

Start by reproducing the embedded doctest example and inspecting the generated documentation and index.html. Determine where documented functions are currently exposed, then add an overview such as a table of contents or function list; done means the generated output provides that overview for the example and larger documented modules.