Add integration tests

[recursion-ninja]

Below is a rough matrix of things we should add for our initial integration tests:

Test Target	Criteria	Metrics	Test type	Script File	Input File(s)
Additive character	Check cost	Linear	HUnit/IO
Non-additive character	Check cost	Discrete	HUnit/IO
Continuous character	Check cost	Linear	HUnit/IO
Sankoff character (DNA)	Check cost	Metric †	HUnit/IO
Sankoff character (Protien)	Check cost	Metric †	HUnit/IO
Sankoff character (65+ alphabet)	Check cost	Metric †	HUnit/IO
Dynamic (DNA)	Check cost	All ‡	HUnit/IO
Dynamic (Protein)	Check cost	All ‡	HUnit/IO
Dynamic (65+ alphabet)	Check cost	All ‡	HUnit/IO
Multi-file input	Check cost	All ‡	HUnit/IO
Weights	Check cost	All ‡	HUnit/IO
Input tree	Check cost	Discrete	HUnit/IO
Input network-single root	Check cost	Discrete	HUnit/IO
Input network-multi-root	Check cost	Discrete	HUnit/IO
Input forest	Check cost	Discrete	HUnit/IO
Wagner RAS	Check cost & topology	Discrete	Golden
Network RAS	Check cost & topology	Discrete	Golden
XML output	Diff output	Discrete	Golden
"Data" output	Diff output	Discrete	Golden
"Dot" output	Diff output	Discrete	Golden
Mismatch graph leaf not in data	Expect failure	N/A	HUnit/IO
Mismatch data leaf not in graph	Expect failure	N/A	HUnit/IO
Duplicate leave in data	Expect failure	N/A	HUnit/IO
Duplicate leaf in graph	Expect failure	N/A	HUnit/IO
No data no graphs	Expect failure	N/A	HUnit/IO

† There should be many metrics tested here: "1-2", "2-1", Leveshtein, L2-Norm (discretized), hamming distance (of string states), etc.

‡ We should tests with the dirscrete metric, the L1-Norm, and all included metrics from (†).

[recursion-ninja]

I've added the integration tests specified. Some defects were revealed that need to be addressed, but the initial integration test suite is in place.