Master Geo-Information Science minor thesis "Evaluating the potential of Sentinel-2 and Landsat image time series for detecting selective logging in the Amazon".
The work is organised into three main directories: data for input and output datasets (placeholders), src for source code and thesis for LaTeX documents. The master branch should only contain text and reasonably-sized images, there may be other branches for binary data.
The working directory is always src (not a subdirectory) and an example of the processing chain is in src/staging/process-data.sh. Due to the large volume of data, you will most likely want to change the locations of your input/output files, how many are processed at once, etc., which is why there is not just one canonical way of processing the data.
For more in-depth descriptions of particular directories, see readme.txt files in them.