Improve code clearness
Move code comment to the correct place
Update Gulpfile to ignore mocha errors

Mocha logs the errors with the reporter itself
Doc script use local node-doc cli
Prepare json objects for saving

Only prepare the json when saving.
Add save options
Add test for requiring a file none existing file
Cleanup code in file parser assert file
Update explanation file parser abosulte require
Cleanup code
Fix cli bug
Add json converter test
Update todo list