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I've been using the Sentinel Level 1C data archive hosted on AWS, maintained by Sinergise.

However, I also need atmospherically corrected data. For that purpose, I use sen2cor, but it relies on the directory structure and metadata of the Sentinel scenes as stored on SciHub. The AWS archive uses a different (albeit simpler and more clear) directory structure.

Is there any utility that either converts the data from the AWS archive to SciHub's original directory structure, or adapts sen2cor for the data that can be downloaded from the AWS archive? As far as I understand, the Sinergise's archive is quite a common source for the Sentinel data, so I believe some work has already been done for that.

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Guys from Sinergise have built the tool that does exactly what you are looking for - it's called

Sentinel-Hub Python packages

Here you can find documentation: http://sentinelhub-py.readthedocs.io/en/latest/

I've tested it with sen2cor and everything was OK.

The instruction to download data as a SAFE structure is like:

product_request = AwsProductRequest(product_id=product_id, tile_list = ['T14PNA', 'T13PHT'], data_folder=data_folder, safe_format=True)
product_request.save_data()

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