--entry-point in subfolder does not work

If the entrypoint file is in a subfolder locally, it attempts to use that subfolder in constructing the entrypoint path on S3.

We should either:
- Truncate the folder when constructing the entrypoint
- Upload the entrypoint to the same subfolder in S3

Start by tracing the CLI's --entry-point handling, including how the local subfolder is used when constructing the S3 path and where the entrypoint is uploaded. Choose and document one of the two behaviors described in the issue, then verify that entrypoints in subfolders are packaged and referenced consistently.

Written by the indexing model from the issue text.