Assuming you have a Jamfile for building your documentation that looks something like:

boostbook standalone
    :
        mylibrary
    :
        # build requirements go here:
    ;

Then add the line:

using auto-index ; 

to the start of the Jamfile, and then add whatever auto-index options you want to the build requirements section, for example:

boostbook standalone
    :
        mylibrary
    :
        # Build requirements go here:

        # <auto-index>on (or off) one turns on (or off) indexing:
        <auto-index>on

        # Turns on (or off) auto-index-verbose for diagnostic info.
        # This is highly recommended until you have got all the many details correct!
        <auto-index-verbose>on

        # Choose the indexing method (separately for html and PDF) - see manual.
        # Choose indexing method for PDFs:
        <format>pdf:<auto-index-internal>off

        # Choose indexing method for html:
        <format>html:<auto-index-internal>on

        # Set the name of the script file to use (index.idx is popular):
        <auto-index-script>index.idx
        # Commands in the script file should all use RELATIVE PATHS
        # otherwise the script will not be portable to other machines.
        # Relative paths are normally taken as relative to the location
        # of the script file, but we can add a prefix to all
        # those relative paths using the <auto-index-prefix> feature.
        # The path specified by <auto-index-prefix> may be either relative or
        # absolute, for example the following will get us up to the boost root
        # directory for most Boost libraries:
        <auto-index-prefix>../../..

        # Tell Quickbook that it should enable indexing.
        <quickbook-define>enable_index ;

    ;

	Tip
	Always send the output to a log file. It will contain of lot of stuff, but is invaluable to check if all has gone right, or else diagnose what has gone wrong.

	Tip
	A return code of 0 is not a reliable indication that you have got what you really want - inspecting the log file is the only certain way.

	Tip
	If you upgrade compiler version, for example MSVC from 9 to 10, then you may need to rebuild Autoindex to avoid what Microsoft call a 'side-by-side' error. And make sure that the autoindex.exe version you are using is the new one.