Question:

When I manually place a .class file in the project's output path directory, it appears to get deleted when I build my project. Why is this happening?

Answer:

When "Synchronize Output Dir" is turned on (Project Properties | Build | Java), all of the class files in the output path directory that do not have source files are deleted during compilation. This is the default setting. You should turn this off when you manually add classes to the output directory.