mrburnette:
The other thing I do is embed all 3rd party libs within the sketch folder. ... Hard disk space is cheap
+1
It also means that your project will work even if a new version of the library emerges elsewhere.
The approach I have devised also deals with two Arduino "features" that I find a real PITA - the need to have a folder named myProject for the file myProject.ino and the inability to refer to INCLUDE files by relative path names - for example so you can include the same file in both the Master and Slave programs.
...R