Script to find overlap in stacked scans

The script does NOT WORK for any eAccounts other than the hard-coded
one, but should allow for detecting the overlap in stacked scans if it
differs from the given value (-c in stacked-scan.py)
Working selection of *all* substacks

Detection of substack number is working.
Also detecting if we work with DMPs or TIFFs.
Now going through all files in a meaningful order.
Working version with writing to log files

This version works (including the input options).
We expect the first of the stacked scans, check for other ones present,
load the bottom image of stack N and compare it to $Percent images from
the top of stack N+1.
The results are displayed (and saved as PNG) and also saved to a log
file in the rec folder.
This should help analyzing the "problem" that the overlap doesn't seem
to be consistent (seen at beamtime for user  e15171 on Oct 27, 2014).

Still missing is the reading of TIFF files and some memory
optimizations.
Using the mean square error is much more robust

Some thinking in the train about the non-robustness lead me to use the
mean square error of the difference image.
Using the MSE is *much* more robust in finding the best slice of stack
N+1 to the stack N.
Cosmetic changes in console output
Consistently get folder name

We got different results if the folder was given with or without the
trailing slash.
Also clean up variable names and give correct help.
Ignore compiled code
Ignoring backup files
Fixed slice vs slicenumber error that Annabelle saw first
Documenting effort

Updating README.md with some help
Merge commit '58576e7'

Conflicts:
	README.md
Merge branch 'master' of https://bitbucket.org/psitomcat/beamline-scripts
Updated README and pulled most recent grecoman
Merge branch 'master' of https://github.com/habi/TOMCAT