Update Dockerfile to use Pip instead of Conda to install application

- Reduce size of app copied to container by adding unneeded
  directories to .dockerignore. E.g Ignore docs, tests, pip build, dist

- Update MANIFEST.ini to include web, emacs interface directories
  Web directory is used by the web interface which will be exposed by
  the docker container

.dockerignore

@@ -1,3 +1,9 @@
 .git/
 .pytest_cache/
 .vscode/
+.venv/
+docs/
+tests/
+build/
+dist/
+*.egg-info/