feat(ingest): Add diagnose-run-ingest.sh diagnostic tool

diagnose-run-ingest.sh

@@ -0,0 +1,130 @@
+#!/usr/bin/env bash
+# diagnose-run-ingest.sh
+# Run from the repo root:  bash diagnose-run-ingest.sh
+# Builds the same fixture the bats test uses and runs run-ingest under `bash -x`
+# so we can see exactly which command makes it exit non-zero.
+
+set -uo pipefail
+
+REPO="$(pwd)"
+RI="${REPO}/skills/ingest/scripts/run-ingest.sh"
+
+echo "==================== ENV ===================="
+echo "bash: $(bash --version | head -1)"
+echo "git : $(git --version)"
+echo "jq  : $(jq --version 2>/dev/null || echo MISSING)"
+echo "py  : $(python3 --version 2>/dev/null || echo MISSING)"
+echo
+
+echo "============ run-ingest.sh on disk ============"
+if [[ ! -f "$RI" ]]; then echo "NOT FOUND: $RI (run me from the repo root)"; exit 1; fi
+echo "-- helper invocations (want 'bash ...'): --"
+grep -nE 'log-append\.sh|scoped-lint\.sh|open-pr\.sh' "$RI"
+echo "-- result emitter (want 'jq -nc'): --"
+grep -nE 'jq -nc?|jq -n ' "$RI"
+echo
+
+echo "============ build hermetic fixture ============"
+T="$(mktemp -d)"
+mkdir -p "$T/nohooks"
+git init --bare -q "$T/origin.git"
+g="$T/g"
+mkdir -p "$g"/{raw/articles,wiki/sources,wiki/entities,wiki/concepts,wiki/queries,wiki/private}
+
+cat > "$g/wiki/index.md" <<'EOF'
+---
+title: "Index"
+type: index
+domain: genome-test
+maturity: stable
+last_updated: 2026-01-01
+private: false
+---
+
+# Index
+
+---
+
+## Sources (`wiki/sources/`)
+*x*
+
+
+## Entities (`wiki/entities/`)
+*x*
+
+
+## Concepts (`wiki/concepts/`)
+*x*
+
+
+## Queries (`wiki/queries/`)
+*x*
+
+
+## Conflicts Pending Review (`wiki/queries/conflict-*.md`)
+*x*
+EOF
+
+cat > "$g/wiki/log.md" <<'EOF'
+---
+title: "Log"
+type: log
+domain: genome-test
+maturity: stable
+last_updated: 2026-01-01
+private: false
+---
+
+# Log
+
+---
+
+## [2026-01-01] CONFIG | init
+- run_id: `init`
+EOF
+
+echo raw > "$g/raw/articles/test.md"
+
+(
+  cd "$g"
+  git init -q
+  git config commit.gpgsign false
+  git config core.hooksPath "$T/nohooks"
+  git config user.email t@t
+  git config user.name t
+  git add .
+  git commit -qm init
+  git branch -M main
+  git remote add origin "$T/origin.git"
+  git push -q -u origin main
+) && echo "fixture commit+push OK" || echo "FIXTURE SETUP FAILED (look above)"
+
+cat > "$g/wiki/sources/test-source.md" <<'EOF'
+---
+title: "Test Source"
+type: source
+domain: genome-test
+tags: [t]
+maturity: draft
+last_updated: 2026-06-04
+private: false
+---
+body
+EOF
+
+cat > "$g/.ingest-manifest.json" <<'EOF'
+{ "raw_source":"raw/articles/test.md","model":"m","reasoning":"r","pr_summary":"s","contradictions":"None",
+  "pages":[{"path":"wiki/sources/test-source.md","summary":"a source","maturity":"draft","status":"created"}] }
+EOF
+
+echo
+echo "============ run-ingest (bash -x) ============"
+cd "$g"
+export KG_LIB_DIR="${REPO}/lib" FORGEJO_URL=http://x FORGEJO_USER=u FORGEJO_TOKEN=t DRY_RUN=1
+bash -x "$RI" genome-test >"$T/out.txt" 2>"$T/trace.txt"
+rc=$?
+echo "EXIT=$rc"
+echo "-- run-ingest stdout (final JSON should be here): --"
+cat "$T/out.txt"
+echo "-- last 25 lines of the trace (the failing command is near the end): --"
+tail -n 25 "$T/trace.txt"