Fuji: make carriage returns optional
Merge pull request #768 from sbesson/rebased/dev_4_4/matlab_performance_test

Improve bfCheckJavaPath performance testing (rebased onto dev_4_4)
merge dev_4_4 -D org -I include -E exclude: PR 746 (CellWorx: ignore thumbnails and missing channel names)
merge dev_4_4 -D org -I include -E exclude: PR 776 (Fuji: make carriage returns optional)