Add sanity checks to parse_coords ( fixes #982 )

Add a couple checks to the coordinates parser, doing this prevents the
parser to load distance matrices seamlessly. Specifically the function
will now check for:
    - First line being the number of vectors.
    - Second to last line being eigenvalues.
    - Last line being the percentage of variation explained.

When these conditions are not mete a `QiimeParseError` exception is
raised; the test suite was extended to check it raises these errors on
different cases.
Remove extra percent sign in coordinates string

This percent sign would have only be needed if the string was being
formatted.
Change exception formatting and if statements

Formatting the exception messages like this will make the transition to
py3k easier.
split the unit tests into different TestCase objects
updated to allow users to test base install versus full install
updated so test output now goes to stdout

previously qiime_config info would go to stdout and test results would go to stdout. this was always annoying as sometimes we want to dump this information to file (e.g., if trying to run the script on some cluster node)
hooked up -v to behave as it does when calling test files directly
first pass at revising install notes
full pass through to update install instructions
cleaned up text - this fixes #1170
better handling of missing dependencies
updated changelog
fixed error in documentation; partially addresses #531
Merge pull request #1241 from gregcaporaso/issue-1170

Issue 1170: define a QIIME base install package
Merge pull request #1178 from ElDeveloper/issue_982

Add sanity checks to parse_coords ( fixes #982 )
fixes #1131
updated link, fixes #972
 fixes #1143
Merge pull request #1248 from gregcaporaso/issue-1131

several small documentation fixes
ported run_script_usage_tests from qcli