Just a small addition to what has been said here.
Yes this is a known issue with Unity, that the project folder gets a bit messy.
Definitely put all your own stuff into a folder, but before you start adding code/functionality. Secondly keep frameworks (Playmaker , Photon) as they are, let them be where they wanna be.
IF you want to move something, do it IN the project window, NOT the Finder (exlplorer in windoze) sometimes Unity will update paths if you do it there, but not if it doesnt know about it.
And most important, do ONE THING AT A TIME; and test before you move something else.
Nice little tool I use is "Build Report" on Asset Store. It shows the size of things in your project, and gives you a report, nice for getting an overview. Currently they are adding functionality that lets you do the opposite, what assets are NOT in use... Even tho Unity doesn't include these elements in a build, its nice to tidy up the clutter...