Change all includes to start at the base instead of assuming the directory where included from.
This makes it more apparent exactly which header has been included, since many have the same name.
This also allows moving all header files out of the src directory.
* Changed the plugin preference API to use luaW_pushscalar() and
luaW_toscalar() to handle preference values.
* Set the __metatable field in the "preferences" table, which blocks Lua
code from changing the metatable and allows developers to query where the
metatable originates.
* Added empty lines to the end of new files.
