Mallet train before init results in cryptic error, fix workflow

[JaimieMurdock]

Add some checks in ldamark/benchmark.py to ensure that all the files Mallet expects are there to anticipate some exceptions. Help the user by suggesting init be run first.

jaimie@compy386:~/workspace/inpho/ldamark 
$ ldamark ap --m mallet --f train --iterations 100 --topics 50
Traceback (most recent call last):
  File "/home/jaimie/anaconda3/envs/py27/bin/ldamark", line 11, in <module>
    load_entry_point('ldamark', 'console_scripts', 'ldamark')()
  File "/home/jaimie/workspace/inpho/ldamark/ldamark/benchmark.py", line 155, in main
    stderr=subprocess.STDOUT).split("\n")[-2]
  File "/home/jaimie/anaconda3/envs/py27/lib/python2.7/subprocess.py", line 219, in check_output
    raise CalledProcessError(retcode, cmd, output=output)
subprocess.CalledProcessError: Command '['/usr/bin/time', '--format', '%e,%U,%S', './mallet-2.0.8RC3/bin/mallet', 'train-topics', '--input', 'out.mallet', '--num-topics', '50', '--output-state', 'mallet_out.gz', '--output-topic-keys', 'mallet_out.txt', '--output-doc-topics', 'mallet_out.txt', '--num-iterations', '100']' returned non-zero exit status 1
# 17:23:34 ✗ (1.673s) 1

jaimie@compy386:~/workspace/inpho/ldamark 
$ /usr/bin/time --format %e,%U,%S ./mallet-2.0.8RC3/bin/mallet train-topics --input out.mallet --num-topics 50 --output-state mallet_out.gz --output-topic-keys mallet_out.txt --output-doc-topics mallet_out.txt --num-iterations 100
Mallet LDA: 50 topics, 6 topic bits, 111111 topic mask
java.io.FileNotFoundException: out.mallet (No such file or directory)
	at java.io.FileInputStream.open0(Native Method)
	at java.io.FileInputStream.open(FileInputStream.java:195)
	at java.io.FileInputStream.<init>(FileInputStream.java:138)
	at cc.mallet.types.InstanceList.load(InstanceList.java:787)
	at cc.mallet.topics.tui.TopicTrainer.main(TopicTrainer.java:199)
Unable to restore instance list out.mallet: java.lang.IllegalArgumentException: Couldn't read InstanceList from file out.mallet
Command exited with non-zero status 1