- Set default output dir to ./output/
- Set format output dirs to lowercased version of the format name
- Create output dirs if they don't already exist
- Register the format name to PhDFormat
- Fix index.sqlite file location
- Fix odd protos (same argument name twice?)
- Fix annoying E_NOTICE
* a new indexing is required if .manual.xml has changed since the last one ('--index false' automatically choose if a new indexing have to be done __ maybe it could be the default option? __)
* added few verbose msgs