science/orthanc: Update to 1.12.9 and unbreak

Fix service start based on:

https://orthanc.uclouvain.be/bugs/show_bug.cgi?id=227

Improve RC script to allow user flags
Fix mismatched db paths
Release notes:

https://orthanc.uclouvain.be/hg/orthanc/file/Orthanc-1.12.9/NEWS

PR: 290458 275624 275623 275622
Approved by: portmgr (blanket, unbreak)