Build each independent tag in main alphafold3 repo

This is a change to the Gitlab CI setup where we no longer need to update our clone of the Alphafold repository before building an image. Instead, the pipeline will clone the repo and determine which tags in the repository do not exist in our container registry. It will then create a separate downstream job for each missing tag, and images will be built at each tagged commit. Those version tags will be used as the image version tags so there is no more confusion about what version of Alphafold is being used. Additionally, the current commit on the main branch will be built and assigned the 'latest' tag. 'latest' in this case will be conceptually the same as a development build. The latest build will be updated each time the pipeline is run while tags will only be added if they do not already exist or a job to build a specific tag is rerun.

.gitlab-ci.yml

 stages:
-  - clone
-  - find_tags
+  - prep_tags
   - build
 
 variables:
   GITHUB_URL: "github.com/google-deepmind/alphafold3.git"
   REGISTRY_URL: "${CI_REGISTRY_IMAGE}"
-  IMAGE_NAME: "alphafold"
+  IMAGE_NAME: "alphafold3"
   REPO_URL: "https://gitlab.rc.uab.edu/api/v4/projects/${CI_PROJECT_ID}/registry/repositories/"
   DOCKER_TLS_CERTDIR: "/certs"
 
-clone_repo:
-  image: alpine:latest
-  stage: clone
-  script:
-    - apk update && apk add curl bash git
-    - curl -s "https://gitlab.com/gitlab-org/incubation-engineering/mobile-devops/download-secure-files/-/raw/main/installer" | bash
-    - source .secure_files/github-key
-    - git clone https://${GITHUB_USER}:${GITHUB_TOKEN}@${GITHUB_URL}
-  artifacts:
-    paths: 
-      - alphafold3/
-    expire_in: 1 hour
+workflow:
+  rules:
+    - if: $CI_COMMIT_BRANCH == $CI_DEFAULT_BRANCH # Only run on main
 
 prep_missing_tags:
   image: ubuntu:latest
-  stage: find_tags
+  stage: prep_tags
   script:
     - apt-get update && apt-get install -y curl git jq
+    - git clone https://${CI_GITHUB_USER}:${CI_GITHUB_TOKEN}@${GITHUB_URL}
     - cd alphafold3
     - git fetch --tags
     - 'REPO_ID=$(curl -s --header "PRIVATE-TOKEN: ${CI_PROJECT_ACCESS_TOKEN}" "${REPO_URL}" | jq ".[0].id")'
@@ -40,6 +31,7 @@ prep_missing_tags:
     - sed -e "s/REPLACE_HERE/${MISSING}/g" template-build-tags.yml > build-tags.yml
   artifacts:
     paths:
+      - alphafold3/
       - build-tags.yml
     expire_in: 1 hour