The other day I had the following error:
Error occurred in deployment step 'Add Solution': Error: Cannot find this file specified in the manifest file: BrandProject_Feature1\addtheme.xml
The feature I had created required an xml file so in the feature1.template.xml file I had the following manifest code:
<ElementManifests>
<ElementFile Location="addtheme.xml" />
</ElementManifests>
However I was having trouble adding a file to the features directory. (BrandProject_feature1). I was getting the above error and deployment was not working so I had to google round for a solution.
The solution, although not obvious, is fairly simple. (Thanks to Henry Chong for pointing me in the right direction)

Delete the Elements.xml file that the new empty element creates, then add your other files to the empty element.

For each file in the element, make sure its deployment type is set to "ElementFile" and its Deployment Location path is set to nothing. This will cause the element files to be added to the root of the feature it is added to.
Now when you test deploy your solution you should not have the error appearing anymore.