Containerization

[kaitj]

This PR adds and updates files required to containerize labelmerge. Also manually deploying this to my docker hub, but we can also add in the necessary github action to deploy to the khanlab org docker hub

• Removed the transforms that don't seem necesssary at this point
• Added .dockerignore to ignore .git (could potentially also include .github)
• Add dockerfile to build a working docker image with the correct entrypoint
  • Used python:3.9-slim-bullseye as base container due to bug with installed verison of python in debian:bullseye (site-packages weren't in the sys.path up to around python3.9.7; this was later patched and this base container contains those fixes)
  • Updated run.py to use /usr/bin/env python3 rather than /usr/bin/python3 which couldn't find python from the base container

Also fixes a bug with the base vs overlay config (this might have been introduced when I rebased from main). The shallow copy (dict.copy()) was causing the base_desc to be replaced by the overlay_desc. To fix this, deepcopy is used.

Proposed changes

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• Bugfix (non-breaking change which fixes an issue)
• New feature (non-breaking change which adds functionalitiy)
• Breaking change (fix or feature that would cause existing functionality to not work as expected)
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• Changes have been tested to ensure that fix is effective or that a feature works.
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