Fragx shaders are executable Fragment Shader files with .fragx or .stoy extensions. They are ordinary GLSL Fragment Shaders with exception of one additional preprocessor directive: "#include". It works exactly as in C/C++ - it "pastes" whole text from other file, in place where it is declared. Apart from that, Syntclipse adds to GLSL special metadata - called Commands - which don't violate the syntax, since they are written only in the comments.
Fragx shaders have limited support for Vertex Shaders (VS). Limited in a sense that you can write your own VS but as input you will always get only 6 vertices, from two triangles representing Viewport quad.
Fragx shaders use by default GLSL 3.3, but it is possible to change it to some other version in Window -> Preferences -> Synthclipse -> Declared GLSL version.