How to organize directories in a small scale project?

Hello guys,

Currently working on a medium sized website and I'm learning a bunch of new tools while working on it. I'm currently using gulp and bower to streamline my process a bit more.

The problem that I'm running into with these tools is that my projects are starting to look a bit messy. With gulp I get a top level directory 'node_modules', with bower I get a 'bower_components' directory.

When I use sass as a gulp component I also need to set up a config.rb and both gulp and bower have their top level .json files.

Also I have my assets marked as 'images', 'css' and 'js' folders. When I use gulp to minify, compress and optimize my assets all these folders will pretty much be doubled.

Ofcourse I know which folders to upload to the actual server but I dread the day I need to hand over my project to another developer who would be in shock of the disorganized project.

Do you guys have any tips or links on how to keep my project tidy and neat when working with all these buildtools and package managers?