Cosmetic changes to ComputeAlignment.py

- merged plot path and aligment path. You want to keep the alignment file
tidy in the Run%i folder anyway.
- improved plot handling, now saves pdfs and all histograms in a root file
Cosmetic changes in pyEudetReconstructionOnly.py

- saving plots as pdfs
- all histograms also saven in a root file
Merge pull request #27 from sredford/master

Cosmetic changes to plot handling in ComputeAlignment and pyEudetReconstructionOnly