The most simple API for a simple command line version is probably found in the classs ‘AxCryptFile’. See Program.cs for support in parsing a command line, and how to register the necessary dependencies in the dependency injection container with ‘TypeMap.Register’.
If you find you need or would like to make any changes to the core code to facilitate things, let me know or submit a pull request.
Where and how did you get the source code? I just downloaded a zip of the tip and it just builds. BERSequenceGenerator.cs is here: https://bitbucket.org/axantum/axcrypt-net/src/5d2decd56c53a185c81aa1fbcc99277d8012d415/BouncyCastle.AxCrypt/src/asn1/BERSequenceGenerator.cs .