diff --git a/.gitignore b/.gitignore
index 9bea4330f0..8f7d5cc5d3 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,2 +1,454 @@
 
 .DS_Store
+aminoacid.owl
+basic-allcycles
+basic-orphans
+basic-orphans.tmp
+basic.json
+basic.obo.tmp1
+basic.owl
+bfo-check.owl
+bfo-check.txt
+bridge-check-caro.owl
+bridge-check-caro.txt
+bridge-check-caro.txt.tmp
+bridge-check-wbbt.owl
+bridge-check-wbbt.txt
+bridge-check-wbls.owl
+bridge-check-wbls.txt
+bridge/bridges
+bridge/uberon-bridge-to-nifstd.obo.tmp
+bridge/uberon-bridge-to-vhog.owl.ofn
+bspo.owl
+chebi.obo
+chebi.owl
+chebi_import.obo
+cl-core.obo
+cl-with-xrefs.obo
+cl-with-xrefs.obo.tmp
+cl_import.obo
+composite-metazoan-basic.obo
+composite-metazoan-dv.txt
+composite-metazoan-dv.txt.tmp
+composite-metazoan.obo
+composite-metazoan.owl
+composite-stages.obo
+composite-vertebrate.obo
+core.owl
+depictions.omn
+depictions.owl
+ext-obscheck.txt
+ext-weak.owl
+ext.json
+ext.obo
+ext.owl
+ext.owl.LOG
+ext2.owl
+external-disjoints.owl
+extra-full-bridge-check-caro.txt
+extra-full-bridge-check-caro.txt.tmp
+full-bridge-check-caro.txt
+full-bridge-check-caro.txt.tmp
+full-bridge-check-wbbt.txt
+full-bridge-check-wbbt.txt.tmp
+full-bridge-check-wbls.txt
+full-bridge-check-wbls.txt.tmp
+go.owl
+GO.xrf_abbs
+go_import.obo
+is_ok
+m1.owl
+materialized.owl
+materialized.owl.LOG
+merged-cycles
+merged-orphans
+merged-orphans.tmp
+merged-stages-xrefs.obo
+merged-stages-xrefs.obo.tmp
+merged.obo
+merged.owl
+metazoan-view.owl
+mirror-caro.owl
+mirror-wbbt.owl
+mirror-wbls.owl
+ncbitaxon.obo
+ncbitaxon_import.obo
+pato.owl
+pato_import.obo
+phenoscape-ext-noimports.owl
+phenoscape-ext.owl
+pr.owl
+pr_import.obo
+quick-bridge-check-caro.txt
+quick-bridge-check-wbbt.txt
+quick-bridge-check-wbls.txt
+reports/stages-metazoan-report.tsv
+reports/uberon_edit-object-properties.csv
+ro.owl
+ro_import.obo
+ro_import.owl.tmp.owl
+run.sh
+seed.obo
+seed.obo.tmp
+seed.owl
+taxon-constraint-check.txt
+trunk/basic.json
+trunk/basic.obo
+trunk/basic.owl
+trunk/bridge/aba.owl
+trunk/bridge/cl-bridge-to-aao.obo
+trunk/bridge/cl-bridge-to-aao.owl
+trunk/bridge/cl-bridge-to-bila.obo
+trunk/bridge/cl-bridge-to-bila.owl
+trunk/bridge/cl-bridge-to-bspo.obo
+trunk/bridge/cl-bridge-to-bspo.owl
+trunk/bridge/cl-bridge-to-caro.obo
+trunk/bridge/cl-bridge-to-caro.owl
+trunk/bridge/cl-bridge-to-ehdaa.obo
+trunk/bridge/cl-bridge-to-ehdaa.owl
+trunk/bridge/cl-bridge-to-ehdaa2.obo
+trunk/bridge/cl-bridge-to-ehdaa2.owl
+trunk/bridge/cl-bridge-to-emapa.obo
+trunk/bridge/cl-bridge-to-emapa.owl
+trunk/bridge/cl-bridge-to-fbbt.obo
+trunk/bridge/cl-bridge-to-fbbt.owl
+trunk/bridge/cl-bridge-to-fma.obo
+trunk/bridge/cl-bridge-to-fma.owl
+trunk/bridge/cl-bridge-to-go.obo
+trunk/bridge/cl-bridge-to-go.owl
+trunk/bridge/cl-bridge-to-hao.obo
+trunk/bridge/cl-bridge-to-hao.owl
+trunk/bridge/cl-bridge-to-kupo.obo
+trunk/bridge/cl-bridge-to-kupo.owl
+trunk/bridge/cl-bridge-to-ma.obo
+trunk/bridge/cl-bridge-to-ma.owl
+trunk/bridge/cl-bridge-to-mfo.obo
+trunk/bridge/cl-bridge-to-mfo.owl
+trunk/bridge/cl-bridge-to-nif_grossanatomy.obo
+trunk/bridge/cl-bridge-to-nif_grossanatomy.owl
+trunk/bridge/cl-bridge-to-og.obo
+trunk/bridge/cl-bridge-to-og.owl
+trunk/bridge/cl-bridge-to-spd.obo
+trunk/bridge/cl-bridge-to-spd.owl
+trunk/bridge/cl-bridge-to-tads.obo
+trunk/bridge/cl-bridge-to-tads.owl
+trunk/bridge/cl-bridge-to-tao.obo
+trunk/bridge/cl-bridge-to-tao.owl
+trunk/bridge/cl-bridge-to-tgma.obo
+trunk/bridge/cl-bridge-to-tgma.owl
+trunk/bridge/cl-bridge-to-vsao.obo
+trunk/bridge/cl-bridge-to-vsao.owl
+trunk/bridge/cl-bridge-to-wbbt.obo
+trunk/bridge/cl-bridge-to-wbbt.owl
+trunk/bridge/cl-bridge-to-wbls.obo
+trunk/bridge/cl-bridge-to-wbls.owl
+trunk/bridge/cl-bridge-to-xao.obo
+trunk/bridge/cl-bridge-to-xao.owl
+trunk/bridge/cl-bridge-to-zfa.obo
+trunk/bridge/cl-bridge-to-zfa.owl
+trunk/bridge/collected-adult-mammal.owl
+trunk/bridge/collected-amniote.owl
+trunk/bridge/collected-anamniote.owl
+trunk/bridge/collected-drosophila.owl
+trunk/bridge/collected-embryonic-mammal.owl
+trunk/bridge/collected-eukaryote.owl
+trunk/bridge/collected-fma.owl
+trunk/bridge/collected-human.owl
+trunk/bridge/collected-mammal.owl
+trunk/bridge/collected-metazoan.owl
+trunk/bridge/collected-mouse-with-stages.owl
+trunk/bridge/collected-mouse.owl
+trunk/bridge/collected-opisthokont.owl
+trunk/bridge/collected-teleost.owl
+trunk/bridge/collected-tetrapod.owl
+trunk/bridge/collected-vertebrate.owl
+trunk/bridge/collected-vhog.owl
+trunk/bridge/collected-xenopus.owl
+trunk/bridge/collected-zebrafish.owl
+trunk/bridge/collected-zfa-plus-mammal.owl
+trunk/bridge/ext-xref.obo
+trunk/bridge/external-disjoints.obo
+trunk/bridge/external-disjoints.owl
+trunk/bridge/hdr-cl-bridge-to-aao.obo
+trunk/bridge/hdr-cl-bridge-to-ehdaa2.obo
+trunk/bridge/hdr-cl-bridge-to-emapa.obo
+trunk/bridge/hdr-cl-bridge-to-fbbt.obo
+trunk/bridge/hdr-cl-bridge-to-fma.obo
+trunk/bridge/hdr-cl-bridge-to-ma.obo
+trunk/bridge/hdr-cl-bridge-to-sctid.obo
+trunk/bridge/hdr-cl-bridge-to-tao.obo
+trunk/bridge/hdr-cl-bridge-to-vhog.obo
+trunk/bridge/hdr-cl-bridge-to-vsao.obo
+trunk/bridge/hdr-cl-bridge-to-xao.obo
+trunk/bridge/hdr-cl-bridge-to-zfa.obo
+trunk/bridge/hdr-cl-ext-bridge-to-zfa.obo
+trunk/bridge/hdr-uberon-bridge-to-aao.obo
+trunk/bridge/hdr-uberon-bridge-to-ehdaa2.obo
+trunk/bridge/hdr-uberon-bridge-to-emapa.obo
+trunk/bridge/hdr-uberon-bridge-to-fbbt.obo
+trunk/bridge/hdr-uberon-bridge-to-fma.obo
+trunk/bridge/hdr-uberon-bridge-to-ma.obo
+trunk/bridge/hdr-uberon-bridge-to-sctid.obo
+trunk/bridge/hdr-uberon-bridge-to-tao.obo
+trunk/bridge/hdr-uberon-bridge-to-vhog.obo
+trunk/bridge/hdr-uberon-bridge-to-vsao.obo
+trunk/bridge/hdr-uberon-bridge-to-xao.obo
+trunk/bridge/hdr-uberon-bridge-to-zfa.obo
+trunk/bridge/hdr-uberon-ext-bridge-to-zfa.obo
+trunk/bridge/uberon-bridge-to-aao.obo
+trunk/bridge/uberon-bridge-to-aao.owl
+trunk/bridge/uberon-bridge-to-aba.obo
+trunk/bridge/uberon-bridge-to-aba.owl
+trunk/bridge/uberon-bridge-to-aeo.obo
+trunk/bridge/uberon-bridge-to-aeo.owl
+trunk/bridge/uberon-bridge-to-bfo.obo
+trunk/bridge/uberon-bridge-to-bfo.owl
+trunk/bridge/uberon-bridge-to-bila.obo
+trunk/bridge/uberon-bridge-to-bila.owl
+trunk/bridge/uberon-bridge-to-bsd.obo
+trunk/bridge/uberon-bridge-to-bspo.obo
+trunk/bridge/uberon-bridge-to-bspo.owl
+trunk/bridge/uberon-bridge-to-caro.obo
+trunk/bridge/uberon-bridge-to-caro.owl
+trunk/bridge/uberon-bridge-to-dhba.obo
+trunk/bridge/uberon-bridge-to-dhba.owl
+trunk/bridge/uberon-bridge-to-dmba.obo
+trunk/bridge/uberon-bridge-to-dmba.owl
+trunk/bridge/uberon-bridge-to-efo.obo
+trunk/bridge/uberon-bridge-to-efo.owl
+trunk/bridge/uberon-bridge-to-ehdaa.obo
+trunk/bridge/uberon-bridge-to-ehdaa.owl
+trunk/bridge/uberon-bridge-to-ehdaa2.obo
+trunk/bridge/uberon-bridge-to-ehdaa2.owl
+trunk/bridge/uberon-bridge-to-emap.obo
+trunk/bridge/uberon-bridge-to-emapa.obo
+trunk/bridge/uberon-bridge-to-emapa.owl
+trunk/bridge/uberon-bridge-to-ev.obo
+trunk/bridge/uberon-bridge-to-ev.owl
+trunk/bridge/uberon-bridge-to-fbbt.obo
+trunk/bridge/uberon-bridge-to-fbbt.owl
+trunk/bridge/uberon-bridge-to-fbdv.obo
+trunk/bridge/uberon-bridge-to-fbdv.owl
+trunk/bridge/uberon-bridge-to-fma.obo
+trunk/bridge/uberon-bridge-to-fma.owl
+trunk/bridge/uberon-bridge-to-go.obo
+trunk/bridge/uberon-bridge-to-go.owl
+trunk/bridge/uberon-bridge-to-hao.obo
+trunk/bridge/uberon-bridge-to-hao.owl
+trunk/bridge/uberon-bridge-to-hba.obo
+trunk/bridge/uberon-bridge-to-hba.owl
+trunk/bridge/uberon-bridge-to-hsapdv.obo
+trunk/bridge/uberon-bridge-to-hsapdv.owl
+trunk/bridge/uberon-bridge-to-ma.obo
+trunk/bridge/uberon-bridge-to-ma.owl
+trunk/bridge/uberon-bridge-to-mba.obo
+trunk/bridge/uberon-bridge-to-mba.owl
+trunk/bridge/uberon-bridge-to-mfo.obo
+trunk/bridge/uberon-bridge-to-mfo.owl
+trunk/bridge/uberon-bridge-to-mmusdv.obo
+trunk/bridge/uberon-bridge-to-mmusdv.owl
+trunk/bridge/uberon-bridge-to-ncit.obo
+trunk/bridge/uberon-bridge-to-ncit.owl
+trunk/bridge/uberon-bridge-to-nifstd.obo
+trunk/bridge/uberon-bridge-to-nifstd.owl
+trunk/bridge/uberon-bridge-to-og.obo
+trunk/bridge/uberon-bridge-to-og.owl
+trunk/bridge/uberon-bridge-to-oges.obo
+trunk/bridge/uberon-bridge-to-oges.owl
+trunk/bridge/uberon-bridge-to-olatdv.obo
+trunk/bridge/uberon-bridge-to-olatdv.owl
+trunk/bridge/uberon-bridge-to-pba.obo
+trunk/bridge/uberon-bridge-to-pba.owl
+trunk/bridge/uberon-bridge-to-sctid.obo
+trunk/bridge/uberon-bridge-to-sctid.owl
+trunk/bridge/uberon-bridge-to-spd.obo
+trunk/bridge/uberon-bridge-to-spd.owl
+trunk/bridge/uberon-bridge-to-tads.obo
+trunk/bridge/uberon-bridge-to-tads.owl
+trunk/bridge/uberon-bridge-to-tao.obo
+trunk/bridge/uberon-bridge-to-tao.owl
+trunk/bridge/uberon-bridge-to-tgma.obo
+trunk/bridge/uberon-bridge-to-tgma.owl
+trunk/bridge/uberon-bridge-to-vao.obo
+trunk/bridge/uberon-bridge-to-vhog.obo
+trunk/bridge/uberon-bridge-to-vhog.owl
+trunk/bridge/uberon-bridge-to-vsao.obo
+trunk/bridge/uberon-bridge-to-vsao.owl
+trunk/bridge/uberon-bridge-to-wbbt.obo
+trunk/bridge/uberon-bridge-to-wbbt.owl
+trunk/bridge/uberon-bridge-to-wbls.obo
+trunk/bridge/uberon-bridge-to-wbls.owl
+trunk/bridge/uberon-bridge-to-xao.obo
+trunk/bridge/uberon-bridge-to-xao.owl
+trunk/bridge/uberon-bridge-to-zfa.obo
+trunk/bridge/uberon-bridge-to-zfa.owl
+trunk/bridge/uberon-bridge-to-zfs.obo
+trunk/bridge/uberon-bridge-to-zfs.owl
+trunk/bridge/uberon-combined-adult-mammal.owl
+trunk/bridge/uberon-combined-amniote.owl
+trunk/bridge/uberon-combined-embryonic-mammal.owl
+trunk/bridge/uberon-combined-eukaryote.owl
+trunk/bridge/uberon-combined-mammal.owl
+trunk/bridge/uberon-combined-metazoa.owl
+trunk/bridge/uberon-combined-opisthokont.owl
+trunk/bridge/uberon-combined-vertebrate.owl
+trunk/bridge/uberon-combined-zfa-plus-mammal.owl
+trunk/bridge/uberon-ext-bridge-to-zfa.obo
+trunk/bridge/uberon-ext-bridge-to-zfa.owl
+trunk/chebi_import.owl
+trunk/cl_import.owl
+trunk/composite-metazoan-basic.obo
+trunk/composite-metazoan.obo
+trunk/composite-metazoan.owl
+trunk/composite-vertebrate.obo
+trunk/core.obo
+trunk/core.owl
+trunk/depictions.owl
+trunk/diffs/def_diffs.rss
+trunk/diffs/Makefile
+trunk/diffs/new_term.rss
+trunk/diffs/obs_term.rss
+trunk/diffs/uberon-combined-diff.txt
+trunk/diffs/uberon-diff.md
+trunk/diffs/uberon-lastbuild.owl
+trunk/envo_import.owl
+trunk/ext.json
+trunk/ext.obo
+trunk/ext.owl
+trunk/external-disjoints.obo
+trunk/external-disjoints.owl
+trunk/go_import.owl
+trunk/homology.owl
+trunk/merged.obo
+trunk/merged.owl
+trunk/nbo_import.owl
+trunk/ncbitaxon_import.owl
+trunk/pato_import.owl
+trunk/pr_import.owl
+trunk/reference/all-combined.md
+trunk/reference/all.md
+trunk/reference/index.md
+trunk/reference/README-editors.md
+trunk/reference/README.md
+trunk/reference/reference_0000000.md
+trunk/reference/reference_0000001.md
+trunk/reference/reference_0000002.md
+trunk/reference/reference_0000003.md
+trunk/reference/reference_0000004.md
+trunk/reference/reference_0000006.md
+trunk/reference/reference_0000007.md
+trunk/reference/reference_0000008.md
+trunk/reference/reference_0000009.md
+trunk/reference/reference_0000010.md
+trunk/reference/reference_0000014.md
+trunk/reference/reference_0000015.md
+trunk/reference/reference_0000016.md
+trunk/reference/reference_0000017.md
+trunk/reference/reference_0000018.md
+trunk/reference/reference_0000019.md
+trunk/reference/reference_0000021.md
+trunk/reference/reference_0000022.md
+trunk/reference/reference_0000023.md
+trunk/reference/reference_0000024.md
+trunk/reference/reference_0000025.md
+trunk/reference/reference_0000026.md
+trunk/reference/reference_0000027.md
+trunk/reference/reference_0000028.md
+trunk/reference/reference_0000030.md
+trunk/reference/reference_0000032.md
+trunk/reference/reference_0000034.md
+trunk/reference/reference_0000035.md
+trunk/reference/reference_0000036.md
+trunk/reference/reference_0000038.md
+trunk/reference/reference_0000039.md
+trunk/reference/references.md
+trunk/reference/test.md
+trunk/reference/top.md
+trunk/reference/uberonref-idranges.owl
+trunk/reference/z.md
+trunk/reports/stages-human-report.tsv
+trunk/reports/stages-metazoan-report.tsv
+trunk/reports/stages-mouse-report.tsv
+trunk/reports/stages-xenopus-report.tsv
+trunk/ro_import.owl
+trunk/subsets/amniote-basic.obo
+trunk/subsets/amniote-basic.owl
+trunk/subsets/appendicular-minimal.obo
+trunk/subsets/appendicular-minimal.owl
+trunk/subsets/circulatory-minimal.obo
+trunk/subsets/circulatory-minimal.owl
+trunk/subsets/cranial-minimal.obo
+trunk/subsets/cranial-minimal.owl
+trunk/subsets/cumbo.obo
+trunk/subsets/cumbo.owl
+trunk/subsets/digestive-minimal.obo
+trunk/subsets/digestive-minimal.owl
+trunk/subsets/efo-slim.obo
+trunk/subsets/efo-slim.owl
+trunk/subsets/euarchontoglires-basic.obo
+trunk/subsets/euarchontoglires-basic.owl
+trunk/subsets/excretory-minimal.obo
+trunk/subsets/excretory-minimal.owl
+trunk/subsets/human-view.obo
+trunk/subsets/human-view.owl
+trunk/subsets/immune-minimal.obo
+trunk/subsets/immune-minimal.owl
+trunk/subsets/life-stages-composite.obo
+trunk/subsets/life-stages-core.obo
+trunk/subsets/life-stages-core.owl
+trunk/subsets/merged-partonomy.owl
+trunk/subsets/mouse-view.obo
+trunk/subsets/mouse-view.owl
+trunk/subsets/musculoskeletal-minimal.obo
+trunk/subsets/musculoskeletal-minimal.owl
+trunk/subsets/nephron-minimal.obo
+trunk/subsets/nephron-minimal.owl
+trunk/subsets/nervous-minimal.obo
+trunk/subsets/nervous-minimal.owl
+trunk/subsets/pulmonary-minimal.obo
+trunk/subsets/pulmonary-minimal.owl
+trunk/subsets/renal-minimal.obo
+trunk/subsets/renal-minimal.owl
+trunk/subsets/reproductive-minimal.obo
+trunk/subsets/reproductive-minimal.owl
+trunk/subsets/sensory-minimal.obo
+trunk/subsets/sensory-minimal.owl
+trunk/subsets/taxon-constraints.owl
+trunk/subsets/uberon-with-isa-for-FMA-MA-ZFA.obo
+trunk/subsets/vertebrate-head.obo
+trunk/uberon-base.owl
+trunk/uberon.json
+trunk/uberon.obo
+trunk/uberon.owl
+uberon-base.owl
+uberon-cycles
+uberon-discv.txt
+uberon-dv.txt
+uberon-dv.txt.tmp
+uberon-obscheck.txt
+uberon-orphans
+uberon-orphans.tmp
+uberon-qc
+uberon-synclash
+uberon-taxmod-314146.owl
+uberon-taxmod-314146.owl.log
+uberon-taxmod-32524.owl
+uberon-taxmod-32524.owl.log
+uberon-taxmod-amniote.obo.tmp
+uberon-taxmod-amniote.owl
+uberon-taxmod-euarchontoglires.obo
+uberon-taxmod-euarchontoglires.obo.tmp
+uberon-taxmod-euarchontoglires.owl
+uberon.obo.tmp1
+uberon.owl
+uberon_edit-cycles
+uberon_edit-obscheck.txt
+uberon_edit-plus-tax-equivs.owl
+uberon_edit-xp-check
+uberon_edit-xp-check.err
+uberon_edit.obo-gocheck
+uberon_edit.obo-iconv
+uberon_edit.owl
+uberon_edit.owl.tmp
+unreasoned.owl
+update-stages
diff --git a/run.sh b/run.sh
index bf03e338eb..026b352466 100755
--- a/run.sh
+++ b/run.sh
@@ -9,4 +9,4 @@
 # we therefore map the whole repo (../..) to a docker volume.
 #
 # See README-editors.md for more details.
-docker run -v $PWD/:/work -w /work --rm -ti obolibrary/odkfull "$@"
+docker run -e ROBOT_JAVA_ARGS='-Xmx25G' -e JAVA_OPTS='-Xmx25G' -v $PWD/:/work -w /work --rm -ti obolibrary/odkfull "$@"