Does `conda env update` remove packages that aren't part of the environment file?

Question

The documentation for conda env update does not really answer this question: After executing the command, is the environment now the same as described in the -f FILE yaml file or does it just add non-existent packages and upgrade outdated packages, leaving manually installed packages?

Answer 1

The --prune option of conda env update is what you are looking for:

conda env update -f file.yml --prune

The option is mentioned in the documentation

Edit: As @MarkLoyman mentions, it has issues since conda 4.4 https://github.com/conda/conda/issues/7279