revamp functions that run executable and associated cleanup - #722

A bunch of major changes included here as discussed in #460:

• Major revamp of all functions that run the Stock Synthesis executable
• check_model() is now check_exe() and supports having an executable in the path (support workflow of having SS executable in the path rather than directory with model files #429). Here's the new "description" section in the function documentation:

  First searches path for the specified executable name and returns the location of that file if found. If not found in path it then searches the specified directory. Linux systems have an existing executable utility /usr/sbin/ss in the path. If exe = "ss" and this file is found by this function, it will be ignored based on the smaller file size relative to the SS3 executable. Linux users who want to use the workflow of having an SS3 executable in their path should name the file something else, such as ss3 or ss_linux.

• run_SS_models() is now run() and has easier defaults and better
  support for having the Stock Synthesis executable in your path (by relying on check_exe())
• Functions have more consistent inputs (e.g. always dir instead of dir, mydir, File, or masterdir, and now defaulting to current working directory)
• Input show_in_console = FALSE will pipe output to a text file keeping R console cleaner while models run
• Adds dependency on 'tidyr'
• Removes never-completed function SSbootstrap()

Here are a couple design choices that I would appreciate additional input on before removing "draft" from this Pull Request:

1. The functions that run the executable use ... to pass additional arguments to run(), such as extras, show_in_console, and skipfinished rather than add a bunch of new inputs to each of those functions (previously not all these options were available or they were controlled by inconsistently named inputs). Benefit is that the function isn't cluttered with as many inputs, but the drawbacks are that these options are less visible and error message associated with incorrect inputs are further removed from the function the user called as in the message where the user calls the jitter function and gets an error from the run() function:

   > SS_RunJitter(dir = "inst/extdata/simple_small", Njitter = 1, nonsense = "blah")
   Error in run(dir = dir, exe = exe, verbose = verbose, ...) : 
     unused argument (nonsense = "blah")
   

2. Can we rename the functions that call the executable as follows to avoid a bunch of inconsistent capitalization? I didn't do this in the pull request because it makes reviewing changes harder (I probably should have held off on renaming run_SS_models() to run() for that reason as well).