Fix documentation build on platforms that do not have tool targets.

- Prevent 'make clean' or its equivalent to remove the generated ScriptAPI.dox and LuaScriptAPI.dox in the 'Docs' subdirectory.
- Always refresh the generated API Doxygen files before building 'doc' target when the tools are available.
- Move document-build binary directory into the respective project main binary directory.
Only use natively built tool for dumping API to doxygen files.

(Pardon the dust)
Merge remote-tracking branch 'upstream/master'

Conflicts:
	Source/CMakeLists.txt