lib: fix config handling

Fixed DebugServer to pass the correct config object to the Session constructor.

Improved error reporting in lib/config.js.
lib: fixed hiding of script files

Modified ScriptFileStorage.findAllApplicationScripts() to exclude files to
hide.

Modified ScriptManager to never hide the main application script file.
README: added FAQ entry for --hidden option

Described what is the format and how to specify the value using
the command-line switch.