Uncouple bridge generation from mappings refresh.

We change the "refresh-external-resources" target so that it still
refreshes (1) the imports, (2) the "local" imports (in fact the local
copies of the foreign ontologies used to build Composite Metazoan),
(3) the externally maintained mapping sets, (4) the externally
maintained bridges; BUT it does not re-generate the bridge files that
are dependent on the refreshed mappings.

The mappings-derived bridges are now expected to be built at release
time (and also at QC time). We build them under MIR=false, so they will
only be built using the locally available mappings (from the last time
they were refreshed), without triggering the download of any remote
resource.

Editors/maintainers can still locally trigger the building of the bridge
files at any time by explicitly invoking the "refresh-bridges" target,
if they want/need to do so.

This does not change anything for whoever is running the refresh
pipeline nowadays: it's still only a matter of invoking
"refresh-external-resources". The only difference is that this won't
trigger a rebuild of the bridge files.

Two benefits: the "refresh imports" PRs will no longer be polluted by
needless changes in the bridge files, in which only the version IRI has
changed; the bridge files will always be generated (at least) at the
same time as the release, so they will always have a correct version
IRI.

Minor cosmetic changes also in this commit:

* "CUSTOM_BRIDGES" is renamed to "EXTERN_BRIDGES", which reflects better
  the true nature of those bridges (it does not really matter that they
  are "custom", what matters is that they are not generated here).

* We use MIR=false, rather than IMP=false, to prevent the downloading of
  any remote resource. This is for consistency with other parts of the
  Makefile.

closes #3438

src/ontology/uberon.Makefile

@@ -1249,8 +1249,8 @@ EXTERNAL_SSSOM_PROVIDERS = fbbt cl biomappings
 # All the sets coming from the above ontologies.
 EXTERNAL_SSSOM_SETS = $(foreach provider, $(EXTERNAL_SSSOM_PROVIDERS), $(MAPPINGDIR)/$(provider).sssom.tsv)
 
-# We only refresh external resources under IMP=true
-ifeq ($(strip $(IMP)),true)
+# We only refresh external resources under MIR=true
+ifeq ($(strip $(MIR)),true)
 
 # FBbt mapping set. We filter it to only keep UBERON-related mappings
 # (CL-related mappings are already bundled with the CL set).
@@ -1296,7 +1296,7 @@ endif
 ifeq ($(BRI),true)
 
 # Those bridges are generated separately (see below).
-CUSTOM_BRIDGES = $(BRIDGEDIR)/uberon-bridge-to-mba.owl \
+EXTERN_BRIDGES = $(BRIDGEDIR)/uberon-bridge-to-mba.owl \
 		 $(BRIDGEDIR)/uberon-bridge-to-dmba.owl
 
 # 1. Prepare the ruleset file.
@@ -1312,7 +1312,7 @@ $(TMPDIR)/bridges.rules: $(SCRIPTSDIR)/sssomt.m4 $(BRIDGEDIR)/bridges.rules.m4
 $(TMPDIR)/bridges: $(SRC) $(IMPORTDIR)/local-cl.owl \
 		   $(MAPPINGDIR)/uberon.sssom.tsv $(MAPPINGDIR)/cl.sssom.tsv \
 		   $(TMPDIR)/bridges.rules $(BRIDGEDIR)/bridges.dispatch \
-		   $(CUSTOM_BRIDGES) | all_robot_plugins
+		   $(EXTERN_BRIDGES) | all_robot_plugins
 	$(ROBOT) merge -i $(SRC) -i $(IMPORTDIR)/local-cl.owl \
 		 sssom:inject --sssom $(MAPPINGDIR)/uberon.sssom.tsv \
 		              --sssom $(MAPPINGDIR)/cl.sssom.tsv \
@@ -1342,8 +1342,8 @@ UBERON_BRIDGE_MBA = "https://raw.githubusercontent.com/brain-bican/mouse_brain_a
 UBERON_BRIDGE_DMBA = "https://raw.githubusercontent.com/brain-bican/developing_mouse_brain_atlas_ontology/main/src/ontology/new-bridges/new-uberon-bridge-to-dmba.owl"
 
 # Only refresh those bridges when we explicitly allow refreshing
-# external resources (IMP=true).
-ifeq ($(strip $(IMP)),true)
+# external resources (MIR=true).
+ifeq ($(strip $(MIR)),true)
 $(BRIDGEDIR)/uberon-bridge-to-mba.owl: $(SRC)
 	$(ROBOT) annotate -I $(UBERON_BRIDGE_MBA) --ontology-iri $(ONTBASE)/$@ -o $@
 
@@ -1408,7 +1408,7 @@ DEPLOY_GH=true
 
 .PHONY: uberon
 uberon:
-	$(MAKE) prepare_release IMP=false PAT=false BRI=true CLEANFILES=tmp/merged-uberon-edit.obo
+	$(MAKE) prepare_release MIR=false IMP=false PAT=false BRI=true CLEANFILES=tmp/merged-uberon-edit.obo
 	$(MAKE) release-diff
 	if [ $(DEPLOY_GH) = true ]; then $(MAKE) deploy_release GHVERSION="v$(TODAY)"; fi
 
@@ -1489,15 +1489,15 @@ clean: clean_uberon
 
 .PHONY: refresh-mappings
 refresh-mappings:
-	$(MAKE) MIR=true IMP=true $(EXTERNAL_SSSOM_SETS)
+	$(MAKE) MIR=true $(EXTERNAL_SSSOM_SETS)
 
 .PHONY: refresh-bridges
 refresh-bridges:
-	$(MAKE) MIR=true IMP=true BRI=true tmp/bridges
+	$(MAKE) MIR=true BRI=true tmp/bridges
 
 .PHONY: refresh-external-resources
 refresh-external-resources:
-	$(MAKE) MIR=true IMP=true BRI=true PAT=false IMP_LARGE=true all_imports all_local_imports tmp/bridges
+	$(MAKE) MIR=true IMP=true BRI=true PAT=false IMP_LARGE=true all_imports all_local_imports $(EXTERNAL_SSSOM_SETS) $(EXTERN_BRIDGES)
 
 
 # ----------------------------------------