The advanced help configuration file is in simple .ini file format. It has an optional section for global settings that might be inherited for each help file, followed by sections for each help file.

Global settings may be put into a section named [advanced help settings]. This means that this name is reserved and it cannot be a help file in any module or theme. The following settings may be set in this section, with the default value (if any) in brackets.

line break (FALSE)
If set, the line break filter will be applied to all help files defined by this module or theme, unless that help file specifically is set otherwise. The line break converts line breaks into br and p tags automatically.
navigation (TRUE)
If set, this navigation will be displayed at the end of the topic: previous topic, Up (parent), next topic.
Specify a css file that will be used for all help files (unless overridden), including the .css extension. This .css file must reside in the help directory along with the .html files, and will not be affected by translation.
May be set to override the module or theme name as displayed in both the module/theme index as well as the navigation and breadcrumb trail. Usually, this is not set, but for some projects you may want to use a more friendly name than appears in the project's .info file.
index name
This may be set to change the name of the module or theme in the module/theme index. It overrides the name setting above, as well as the project's name in its .info file.
hide (FALSE)
This may be used to hide a module or theme in the module/theme index. This is particularly useful for modules who insert their help files into the hierarchy of another module or theme, as might be done by modules that extend Views or derived themes that extend base themes like Zen. By setting this to TRUE the project will not appear as its own entry.

Each section after that will correspond to a single help file for a single topic. It starts with the topic name in square brackets (e.g. [ini-file]). The following settings may be set for each file/topic, with the default value (if any) in brackets.

The title of the topic, presented to the user and used in links. If you have special characters in your title, be sure to enclose it in quotes. (This setting is currently not optional.)
file (topic name)
The filename, without the .html extension, used for the file with the help text for the topic. This is optional; if not specified, the topic name wil be the file name.
weight (0)
The weight, used for sorting topics on the administration page. The default is 0 (zero) if unspecified. Items with the same weight are sorted alphabetically.
The topic ID to use in a hierarchy; children will be listed beneath parents in the topic list, and will have the parent in their breadcrumb trail. You may parent this topic to a topic in another module or theme by using module%topic or theme%topic as the identifier, where module or theme is the project's short name. For example if parent is set to, 'views%display', the topic will be regarded as a child of the display topic in the Views module.
line break (FALSE)
Set the line break filter for this topic. Set to FALSE to disable the line break filter if this has been turned on in the global settings.
Specify a css file that will be used for this file. This .css file must reside in the help directory along with the .html files. This will override any .css file added by the global settings.
popup width (500)
The width in pixels of the popup window.
popup height (500)
The height in pixels of the popup window.

For example, here is a version of the file:

title = README
weight = -11

title = Using advanced help
weight = -10

title = Translating advanced help

title = Help .ini file format
line break = FALSE

title = Why advanced help?
line break = TRUE