fix CP2K

Signed-off-by: Fotis Georgatos <fotis.georgatos@uni.lu>
fix ABySS & BFAST sources lines

Signed-off-by: Fotis Georgatos <fotis.georgatos@uni.lu>
fix flex, libpng & netCDF sources

Signed-off-by: Fotis Georgatos <fotis.georgatos@uni.lu>
Merge pull request #281 from fgeorgatos/fix_SOURCES_part2

Fix sources part2