All self written docs are created by writing texinfo files. texinfo is the documentation tool of the GNU project http://www.gnu.org. texinfo files can be processed by TeX or by makefinfo. See http://www.texinfo.org for more details.
Out of texinfo doc's can be created HTML files or info files.
For all commands and applications and other texinfo files are generated. The reasons for using texinfo are well enough explained in texinfo's info:
TeX works with virtually all printers; Info works with virtually all computer terminals; the HTML output works with virtually all web browsers. Thus Texinfo can be used by almost any computer user.
Out of the self written and generated texinfo doc's siliconBrain generates HTML doc's. Because the idea is, to support open source projects, the source tree is also HTMLified. The complete HTML is generated in a local WEB, which is beyond the distribution/documentation subdir. This then is automatically installed into a WEB target.
The complete source tree (without the temporary and distribution subdir) is HTMLified. That is, for each directory siliconBrain generates a HTML file with a link for each file. This dir is a syntax highlited version of the ls output. Here each file is a link to an HTMLified version of that file.