added failing test

to help debug issue #7
added test of passing an alternative finder function

this shows how to handle the issue #7 use case with no changes to the MinimalFastaParser code. I don't think issue warrants an code change, but since I wrote this test it doesn't hurt to add it to PyCogent.
Fixed logdet distance and added paralinear. Contributed by Ben Kaehler.

[CHANGED] also turned back on a bunch of tests I had iadvertently inactivated
    some time ago.

Thanks for the fix Ben!
initial commit of FLASh app controller
test of second commit of FLASh app controller
added all paramters
removed MixedParameter
indentation fixes
started convenience functions
added to convenience functions. started to add class methods
added synonyms dict and getHelp method
removed extra '}'
changed getHelp doc string'}'
added a few private methods
removed some import statements
edited '-d' value param
changed miseq suggested max overlap param
updated code in '_get_result_paths'
explicitly check for absolute file paths in 'default_assemble'
changed working_dir to WorkingDir in 'default_assemble'