Include ecoip_plot.R in the package
Don't include the bibliography for now
Make an R package

* CMakeLists.txt: New building logic to generate the R package.
* docs/man/EcoIP-package.Rd: New documentation file for package.
* docs/man/ecoip_exec.Rd: New doc file for ecoip_exec function.
* docs/man/ecoip_plot_exec.Rd: New doc file for ecoip_plot_exec func.
* src/R/colorTrans.R: Expect the sources to be under R from now on.
* src/R/naiveBayes.R: Likewise
* test/test_color.R: Likewise
* test/test_mask.R: Likewise
* test/test_nbm.R: Likewise
We no longer need to output with SVG
Pass all arguments to EcoIP as function arguments not command Args.
Add some FIXMES
Implement all ecoip's functionality in functions.

With this change we removed the use of getopt in ecoip.R. We might use it in
ecoip executable.
* docs/man/ecoip_exec.Rd: Deleted man file for removed function.
* docs/man/eip.genOutput.Rd : New function. Creates the signals and videos
* docs/man/eip.histcmp.Rd : New function. Creates the histogram comparisons.
* docs/man/eip.nbm.Rd: New function. Creates the Naive Bayesian Model. It can save
the model or return it to the R session.
* docs/man/eip.showModel.Rd: New function. Shows the contents of a model
object. It also recieves model files.
* src/R/ecoip: We put all the code related to getopt in this file. We commented
it out.
* src/R/ecoip.R: The 4 new functions live in this file.
Use foreach to reduce the number of lines
Include sample images.

* CMakeLists.txt: Put the sample images in the Rpackage.
* docs/man/eip.genOutput.Rd: Add example code to the man page.
* docs/man/eip.histcmp.Rd: Likewise.
* docs/man/eip.nbm.Rd: Likewise.
* docs/man/eip.showModel.Rd: Likewise.
Address a documentation warning.
Fix minor bug. strop -> stop
Make the manual equal to the function call
Remove the getopt package requirement
Code ecoip so it can continue to work from the shell
Create a plotting function from ecoip_plot

* CMakeLists.txt: Remove ecoip_plot_exed from the exported R obejcts.
* samples/images/treete/01.jpg -> samples/images/treete/2000-12-01.jpg: Changed
file name so the examples can work.
* samples/images/treete/02.jpg -> samples/images/treete/2000-12-02.jpg: Likewise
* samples/images/treete/03.jpg -> samples/images/treete/2000-12-03.jpg: Likewise
* samples/images/treete/04.jpg -> samples/images/treete/2000-12-04.jpg: Likewise
* samples/images/treete/05.jpg -> samples/images/treete/2000-12-05.jpg: Likewise
* samples/images/treete/06.jpg -> samples/images/treete/2000-12-06.jpg: Likewise
* samples/images/treete/07.jpg -> samples/images/treete/2000-12-07.jpg: Likewise
* samples/images/treete/08.jpg -> samples/images/treete/2000-12-08.jpg: Likewise
* samples/images/treete/09.jpg -> samples/images/treete/2000-12-09.jpg: Likewise
* samples/images/treete/10.jpg -> samples/images/treete/2000-12-10.jpg: Likewise
* samples/images/treete/11.jpg -> samples/images/treete/2000-12-11.jpg: Likewise
* samples/images/treete/12.jpg -> samples/images/treete/2000-12-12.jpg: Likewise
* src/R/ecoip.R : Add new function eip.plot and helper to take care of the
plotting
* docs/man/eip.plot.Rd: New docuementation file.
* src/R/ecoip_plot: Put all the getopt logic from ecoip_plot.R into this file.
* src/R/ecoip_plot.R : Remove unneeded file.
* docs/man/ecoip_plot_exec.Rd: Remove unneeded documentation file.
Fix bug. fixes #38
Fix bug. fixes #39