I'm developing a bot using the online editor, to add and remove files I was first using the OneDrive continuous integration then tried using BitBucket.
Using OneDrive adding files seemed to work but recently I wanted to also remove some files. I removed them from my local drive, waited for it to sync up to onedrive (I checked and they had gone from the web view) and then did a sync from the bot console.
The new files were created but the files I had deleted are still in the bot and screwing up the compilation.
More recently I have setup a BitBucket account and created everything there, connected it up etc and deployed to the bot account and it also doesn't change any of the code.