If you want the platform to crawl a sub directory, then you will need to add that as a "site" in its own right. This might mean effectively that you have both the main domain or (www) sub domain in your My Sites table, along with the site + sub directory:
As you can see from the above screenshot, you will also need to set your sites up in this way if your site supports foreign languages in this way (by keeping language-specific content in directories).
However, using the above example, if the site had language specific sub domains - fr.analyticsseo.com e.g. - then it would have been necessary to add the site exactly as the sub domain is setup.
There are some implications to doing this:
\ Spidering - we will only spider from that directory*** onwards, i.e. the spidering part of the platform will look for internal links with the same directory structure (so using the above example, links beginning "www.analyticsseo.com/fr"). **NB: You will need to ensure that the directory you enter returns a page and not just a blank screen (usually an index.html page), as it will need to follow links from that point on - it's not just going to take a sub directory and start guessing what the sub directories to that are called!
\ Keyword Ranking* - the system will still check for ranks for your root domain and your main sub domain (www) - i.e. It will not carry out directory-specific ranking checks as it could potentially miss rankings for URLs from different directories or sub-domains which you would want to know about.
* Backlinks - the system will import link details from Majestic SEO for your sub directory only!
* Top Pages - the system will analyse the top pages from within the directory you have specified!
* Technical Healthchecks - the system will still look for sitemaps, robots.txt files and Custom 404s, based on your TLD. In the above example, it would be looking for www.analyticsseo.com/robots.txt and not www.analyticsseo.com/fr/robots.txt.
* Google Analytics and Google Webmaster Tools data - you can create specific GA and GWT profiles for this kind of website structure. Simply create a filtered profile (not an Advanced** Filter)**, add the site on separately and choose the filtered profile you have setup for that directory. We will then import traffic, conversion, revenue numbers for just that profile, i.e. For just that directory.