We have an application to convert manuals/documents in PDF format to structured xml/html content, and we want to build an export module to allow to bulk upload generated content to Alfresco Wiki, can it done with CMIS ?
Yes, Alfresco wiki pages are instances of cm:content which means in CMIS they are instances of cmis:document. You should add the cm:titled aspect to wiki pages and set the cm:name and cm:title to the page name.
The folder that the wiki pages reside in is an instance of cm:folder (cmis:folder) with the st:siteContainer aspect added and the cm:name and st:componentId set to "wiki".
Regarding your second question, if you are asking what software is used to produce the docs.alfresco.com site, I believe it is Eclipse Infocenter, but I'm not 100% certain.