Fix the image build, and stop the fallback refusing Clusters

[Robbie1977]

Fix the image build, and stop the fallback refusing Clusters

Two defects in #108 as merged. main's Docker Image CI is currently red on the first of them.

The build

The Dockerfile checked both clones out at master, but the two repositories disagree — VFB_json_schema_indexer's default branch is main and VFB_json_schema's is master — so the indexer checkout failed with pathspec 'master' did not match any file(s) known to git.

The refs now default to the sentinel default, which skips the checkout and keeps whatever the clone gave us. An explicit --build-arg INDEXER_REF=<sha> still pins exactly as before. Naming a branch here would break again, silently, the day either default is renamed.

(The first failure on this hunk was a different one and is now moot: VFB_json_schema_indexer was a private repository, so the anonymous clone could not authenticate. It is public as of today.)

Clusters

EXCLUDED_ID_PREFIXES was applied to every id, but that list is copied from the anatomical individual indexer's parameter query:

MATCH (i:Individual) WHERE NOT i:License AND NOT i:DataSet AND NOT i:pub
  AND NOT i:Template AND NOT i:Cluster
  AND NOT i.short_form starts with 'VFBc_' AND NOT i.short_form starts with 'FBlc' ...

FBlc ids are Clusters, which ClusterTermInfoQueryIndexer owns — so as written the fallback refused to rebuild any Cluster document. That is the one term type whose query exists only in the indexer and not in QueryLibrary, and therefore the one this feature can least afford to drop. Renamed ANATOMICAL_EXCLUDED_ID_PREFIXES and applied only on that branch.

How to test

FBlc0006125 → "scRNAseq_2018_Davie_FULL_seq_clustering_adPN_neurons", types include Cluster

Verified live. The clone/checkout chain was also run through sh with both a default and an explicit ref. Unit tests still pass with and without the indexer checkout present.

[github-actions]

⚠️ 165 test(s) skipped — VFB backend was unreachable

The full suite ran, but 165 test(s) were skipped because the VFB backend (Neo4j / SOLR / Owlery) did not answer during this run.

These are not failures and not a problem with this branch — but those queries went unverified, so a green check here is an incomplete run.

To re-run: open this workflow run and click Re-run all jobs once the backend is healthy (re-running the “Run completeness” check itself does nothing — it has no job behind it).

3 failed, 623 passed, 165 skipped, 339 warnings in 840.30s (0:14:00)

_{Posted automatically. This comment is removed once a run completes with zero skips.}