Checkpoint connector bugfixes
[🤖]: Hi @jstjohn 👋,

I just wanted to let you know that, you know, a [CICD pipeline](https://github.com/NVIDIA/NeMo/actions/runs/11110721974) for this PR just finished successfully ✨

So it might be time to merge this PR or like to get some approvals 🚀

But I'm just a 🤖 so I'll leave it you what to do next.

Have a great day! 

//cc @ko3n1g CI seems to have an issue with CI assets; will retry it later. [🤖]: Hi @jstjohn 👋,

We wanted to let you know that a [CICD pipeline](https://github.com/$REPOSITORY/actions/runs/$RUN_ID) for this PR just finished successfully

So it might be time to merge this PR or get some approvals

I'm just a bot so I'll leave it you what to do next.

//cc @pablo-garay @ko3n1g This needs https://github.com/NVIDIA/NeMo/pull/10786
# What does this PR do ?

Get checkpoint connector working for bionemo (see https://github.com/NVIDIA/bionemo-fw-ea/pull/180)

# Changelog 
- Use new nemo2 standard `/weights` and `/context` subdirectory scheme so checkpoint loaders work properly with checkpoints created by this method.
- dedup [ckpt_to_dir](https://github.com/NVIDIA/NeMo/pull/10647/files#diff-8b8117bc8b07d1fa52030c25e6a7c7920aafa31780e2665ec5fe63939c11a622L272)
- Other changes necessary to allow checkpoint transformation outside of training resumption.