Change sim inputs to use random dwells of sufficient length

Changes to make_sim_inputs.py:
The make_sim_inputs.py file is essentially rewritten to:
    - Use random dwells of sufficient length (default = 1ks)
    - Encapsulate generation of inputs in class form for (among the other benefits classes offer):
        - Readability
        - Easier/more explicit passing of arguments
        - More explicit object isolation
    - Reduce some redundant operations (e.g. finding suitable starting dwells more often than necessary)

Changes to __init__.py:
__init__.py is modified to:
    - Use the new sim inputs generation method and to
    - Allow the user to specify minimum starting dwell length

Change to VERSION:
Version is changed from 0.5.1 to 0.6

Signed-off-by: Matthew Dahmer <matthew.dahmer@gmail.com>
Update docs, clarify wording in comments
Fix formatting and clarify wording
Undo unintentional modification to import statements
Refactor sim input generation into fuction from class, Add max dwells keyword
Update docs to reflect keyword 'max-dwell-num'
Minor format cleanup
Merge pull request #7 from sot/change_sim_inputs

Change sim inputs