Initial commit to my fork. In this I am mostly playing around with atom to figure out how I might implement the run configuration feature.

I am wanting to have it be
1. Run the command by keybind etc
2. Dialog pops up with fields
3. Run normal script with those options
Added a framework for storing options which are persistent for the life of the view. Currently there is no frontened way to change them, but testing them by changing the code indicates that the optiosn properly change the running of the command.

The next step will be to implement a frontend to be able to change the options.

Rather than going for a customized run option, I am going to go in the direction of a command which will change the options that the normal run uses. This later can be extended to pull the default options from existing configuration files.
Added the UI for configuring run options. It currently is not linked to any backend and still needs some more work to display all necessary options.
I added better styling to the view using the style guide provided by atom.

I also changed the behavior. I have a method which toggles the options on and off. The regular run insures that this is toggled off. When the option command is run it runs with this option toggled on. This should make sure that there is one script view per code file but allow easy changing between seeing it and not and allow for creation of a close button.

I am working on passing the values of the input into the option framework that I setup. The problem that I have right now is that when I type something into a text input, I cannot backspace the input. I don't know why this is happening but it seems related to a text input element. Once that is fixed, it should be easy to pass the arguments collected for configuration, add a save/close button, and be ready for some testing
Completed hooking up the backend to the UI. You can now modify the cwd, command arguments, and script arguments via cmd-shift-i.

Basic functionality works, but more work is needed on making the UI smoother.
Made changes on the css names to use all dash style instead of camel case
Changed .css calls to .show() and .hide(). Also used shorter notation for if statement from if mode !=null to if mode?
Removed debugging console.log statements
added myself as a contributor
removed unnecessary return statements
renamed script:options to script:run-options
Changed the text from Script Arguments to Program arguments and added a run button
Simplified the toggle code to use jquery .toggle() and the ability to force with .hide() or .show() still. Behavior should still be the same so far
Changed the flow so that running the options doesn't run the program. It instead empties the panel and says its configuring options.

To run the script, there is a run button which will save the options, close the option dialog, and run the program.

For some reason I can't get it to appear without the script window already being open
Cleaned up more from last commit removing unnecessary default arguments
Added the options configuring to the script menu.

Fixed the bug where it would not run without script already being open, which was failing to rename teh activation event from script:run-options.

This now should be ready for some more review
Caught a bug where running wouldn't save the options first
Changed the naming of options to avoid a name collision
collapsed multiple divs into one
Refactored the options view to a better name and separated it from the script view. Currently trying to get options to pass between views