Plug-in Manifest Builder or in short, manifest builder is contributed by PDE through org.eclipse.pde.core plug-in. This is the builder that would compile your plug-in each you change plug-in dependencies, modify build.properties, change classpath, add or remove libraries, save your code/classes. It compiles the plug-in and validate that required files (plugin.xml, etc) are in place and in correct shape.

It is one of the two builder that any plug-in/fragment or equinox bundle project will have by default. It is a bit paranoid builder. If it can not understand any change (resource delta) it will go for full build of the project.

The Plug-in Manifest Compiler preference page has a bunch of options that control the problem severity generated by the builder.

 

From http://blog.ankursharma.org/2011/07/plug-in-manifest-builder.html