Extra files with same name get clobbered

Hi,

I've got a project with two 2 directories that each have a README. When I run yard it appears to output ok, but when viewing the docs it will show both files in the file list, but only one file exists in the document directory and and this is used when following the link for either file. I'm able to recreate this very easily with a toy project of 2 subdirs and a README in each.

I've started to look into this, but I'm not yet entirely sure where the problem is as I'm just getting my head into the code. I've started rejigging the specs for this to help, which so far involves replacing the instance variables with a `let`, and adding some `context`s. The main action will be around the block beginning `describe 'Extra file arguments' do` which is at line 539 in my code. I thought I'd open a pull request ahead of time so we could discuss it.

I was wondering if you could point me to where in the code "file." is prepended to the file name. So far I've not found it.

Regards,
Iain