As dop2000 says you cannot modify project files from within your game. This doesn't stop you from being able to keep your changes though.
If you want to modify the files only for that user, you can save your changes to localstorage. When the game starts you can check if a revision exists in localstorage and load that instead of the project file.
If you want to actually put your changes back into the project the easiest way is to download the JSON object from your game, and then back in the editor replace the project file with the JSON file you have just downloaded. This basically makes your game a custom authoring tool for that file.