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CA merging GaudiConfig2 fixes

Teng Jian Khoo requested to merge khoo/athena:master-CA-GaudiConfig2-fixes into master

Attn @wlampl, @tbold,

I found I had to make a number of changes to make merging of sequences with many shared components work again (specifically, these are the non-jet-specific bugfixes that were needed for JetRecConfig/share/JetRecTestCfg.py to run).

The changes in AtlasSemantics were needed because there were ToolHandles that were set to empty i.e. '', which caused merging to fail.

Edited by Teng Jian Khoo

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