Update alpha branch

[eunos-1128]

This pull request includes changes to the io.github.pemsley.coot.yaml file to update module configurations and dependencies. The most important changes involve the reconfiguration and update of the gemmi module and the update of the coot module commit reference.

Dependency and module updates:

• Re-added the gemmi module with updated source tag v0.7.1 and moved it under the cleanup: section.
• Removed the gemmi module from its previous location under the modules: section.
• Updated the coot module commit reference to d118c4049e847affe558bd4f56915f9fbcb292cb.

[Copilot]

Copilot reviewed 1 out of 1 changed files in this pull request and generated no comments.

[flathubbot]

Started test build 193628

[flathubbot]

Build 193628 successful
To test this build, install it from the testing repository:

flatpak install --user https://dl.flathub.org/build-repo/176850/io.github.pemsley.coot.flatpakref