Path validation for pid_path/log_path. Validation for GALAXY_RUN_ALL env var. Added error checking.
Changed RUN_GALAXY_ALL=0 to unset RUN_GALAXY_ALL because run.sh checks if the variable is set or not.
Merge pull request from Iyad Kandalaft: improve robustness & allow additional args

Iyad's changes include:
- dealing with existing GALAXY_RUN_ALL setting
- allows additional arguments for run.sh to be passed via command line
- checks for existence of PID_PATH and LOG_PATH (and creates them if not found)
- confirm process has stopped if PID file still exists after --stop-daemon