Change indentation and code formatting

The main changes that happened over the code were the following:
    - All the code is now indented using tabs
    - All if/else/for/try/ statements use curly braces
    - Indentation was modified to be consistent all along the file
    - Commented code was removed
    - Unnecessary trailing spaces were removed
Change global variable to be prefixed with a g_

This changes brought the need to update format.py and in turn the test
suite for this moduel. The main emperor file was updated accordingly,
most of the bigger changes happened here:
    - Removed unnecessary variables
    - Grouped global variable declaration and descriptions
    - Update code accordingly
    - Minor random format fixes to the file
Change variable names that lacked a g_ prefix

The test suite need to be modified to support these changes as well as
the emperor.js file.

This should fix #34
Add g_ellipsesDimensions declaration by default

Having this variable declared only when the user is making a jackknifed
plot will make emperor.js fail because the variable doesn't exist at
least now it exists as an empty variable.

Test suite was updated accordingly.
Remove ability to delete "all-equal" categories

Some categories from the mapping file were deleted if those didn't have
at least 2 different values between samples. This was inconsistent with
the script interface.

Unncessary statements were also removed.
Change the code to be standard through the module

Some of the general changes that happened:
    - Make the names of some functions more descriptive.
    - Add a description to all the functions
    - Use camelcase for all the function names
Merge branch 'master' of git://github.com/qiime/emperor into issue_34
Change function name & remove commented HTML
Allow excluding categories in -b and -a -- fix #47

The way the script was working, it was first filtering the "--color_by"
categories and then adding the --custom_axes; this has been corrected.

This fix #47.
Merge pull request #50 from ElDeveloper/issue_47

Allow excluding categories in -b and -a -- fix #47
Merge pull request #45 from ElDeveloper/issue_34

Clean up emperor.js -- close #34
Change script usage examples
Add execution of script usage tests in all_tests

A test data directory has been added to the repository containing sample
data to run script usage tests.

all_tests.py has been update to by default execute all of the script
usage tests in the scripts directory. Some changes that happened in this
script:
    - Variable name clean-ups
    - Option name changes
    - Addition of options to specify a scripts dir as well as a test
      data dir, both of these are optional, if not provided the script
      will try to automatically find these.

This fixes #44
Change script interface to not take test_data_dir

There is no need to take this path since it exists in the tests
directory and the script will only exist in the tests directory.
Merge pull request #51 from ElDeveloper/issue_44

Add test data to emperor -- fixes issue 44