Migration of changes from rel21 to rel22 and other MT related fixes

• Fixed several bugs (left over from Service -> Tool conversion)
• Re-indenting everything
• Removed some ancient and cryptic comments
• Added some more debug messages
• Updated copyright for some python scripts
• Implementing a couple of improvements which have been only merged to rel 21
  • by default all noisy strips are written to COOL
  • efficiency summary files shows also side index
  • adopt changes to histogram name in input hist file