Circuitscape/Circuitscape — pull request #5 by tanmaykm (2013-11-05 23:08:10+00:00)
Title: Merged all modes and modules to a common scheme

This PR merges all modules and both network and raster modes (for pairwise module) into a common scheme. This avoids duplication and has hopefully made the code more modular.

The primary changes are:
- CSHabitatGraph class to represent the habitat map/graph and short circuit regions.
- CSOutput class to represent manipulations on voltage and current maps before they are written as outputs
- CSFocalPoints class to represent a set of focal points and associate logic to work with them
- All modules modified to work with the above abstractions

All tests are passing and performance does not seem to be affected. I had to change the output file names to bring them to a common scheme, hence lot of files under `verify/baseline_results` needed to be renamed.

If these changes look OK, I shall fix the setup routines next so that the changes so far are not broken in any way and can be merged to the master branch. Will take up parallelizing post that.