Part-FCL no longer contains the term commander, except in some of the syllabus templates.
Part-OPS refers to commander in the usual manner, but the definition is missing.
Actually, it's not missing, just well hidden
Annex I to Regulation 965/2012 - Definitions
(96) ‘pilot-in-command’ means the pilot designated as being in command and charged with the safe conduct of the flight. For the purpose of commercial air transport operations, the ‘pilot-in-command’ shall be termed the ‘commander’;