Draft: clean, refactor and version common directory

Changes:

• remove unused global/positions.xml
• move PipeGeomParams.xml and PipebeforeMagGeomParams.xml from common directory to Pipe directory
• refactor definations part from common.xml
• refactor Regions from common.xml
• refactor materials parts, close #59

Questions & Following

is the debug directory needed for the released version? Even for the trunk version, it looks like the checks are only happening for run3.

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Validated by

• Core Software
• RTA
• Simulation