Rewrite load_from_server to accept a callback function that handles the data. This can be a general function to set up the tool given we're starting from an entire stack, which can be reused in the code that handles file upload (filereader, reader.onload).
This could even be a generic initialiser, similar to resetStack() in app_binary, which will create a blank slate if it isn't passed any data. This would replace resetStack() and be called in cy.ready instead of explicitly setting the window variables before starting cytoscape.js. The initialiser could also handle the esynOpts object to determine what to change about the page layout (disable buttons, change project name text, change button text, etc.). This could use the existing load_from_stack?