The whole project folder will sync to the mpy board, you can upload the folder with a single command.
mpypack will only upload the necessary files, so a big project in a folder will not be a problem.
And it can also compile the code automatically before upload (with mpy-cross).
Details on github: mpypack
The useage is simple, to build the project:
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mpypack build
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mpypack -p [port] sync
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mpypack sync; mpypack repl