feat: enhance ingest workflow with validation, PR control, and robustness

skills/ingest/scripts/open-pr.sh

@@ -80,7 +80,15 @@ case "$code" in
     echo "PR opened: ${url}"
     ;;
   409)
-    echo "open-pr: a PR for '${branch}' already exists — push updated the branch." >&2
+    # PR already exists — fetch it so the orchestrator still gets the URL.
+    existing="$(curl --max-time 15 -s -H "Authorization: token ${FORGEJO_TOKEN}" \
+      "${FORGEJO_URL}/api/v1/repos/${FORGEJO_USER}/${repo}/pulls?state=open" \
+      | jq -r --arg b "$branch" '.[] | select(.head.ref==$b) | .html_url' | head -n1)"
+    if [[ -n "$existing" && "$existing" != "null" ]]; then
+      echo "PR opened: ${existing}"
+    else
+      echo "open-pr: a PR for '${branch}' already exists (push updated the branch)." >&2
+    fi
     exit 0
     ;;
   401)

skills/ingest/scripts/run-ingest.sh

@@ -25,6 +25,18 @@ command -v jq      >/dev/null 2>&1 || { echo '{"status":"error","reason":"jq mis
 command -v python3 >/dev/null 2>&1 || fail "deps" "python3 missing (needed by index-append.py)"
 [[ -f "$manifest" ]] || fail "manifest" "manifest not found: ${manifest}"
 
+# --- validate the manifest BEFORE trusting any field (LLM output is stochastic) ---
+# 1) well-formed JSON object with a string raw_source and an array of pages
+jq -e 'type=="object" and (.raw_source|type=="string") and (.pages|type=="array")' \
+  "$manifest" >/dev/null 2>&1 \
+  || fail "manifest" "invalid manifest: need object with string raw_source and array pages"
+# 2) every page.path must be a string, live under wiki/, and contain no '..' (no traversal)
+if jq -e '[.pages[].path
+            | select((type!="string") or (startswith("wiki/")|not) or test("\\.\\."))]
+          | length > 0' "$manifest" >/dev/null 2>&1; then
+  fail "manifest" "unsafe page path (must be a string under wiki/, no '..')"
+fi
+
 # --- read manifest scalars ---
 raw_source="$(jq -r '.raw_source'             "$manifest")"
 # model name comes from the orchestrator/wrapper (INGEST_MODEL); the agent cannot know its
@@ -88,6 +100,7 @@ lint_out="$( bash "${SCRIPTS}/scoped-lint.sh" "$genome" "${all_paths[@]}" 2>&1 )
 
 # --- 4. assemble the PR body (manifest tables + lint results) ---
 body="$(mktemp)"
+trap 'rm -f "$body"' EXIT      # auto-clean on any exit (success, fail(), or crash)
 {
   echo "## Summary"
   echo "$pr_summary"
@@ -107,13 +120,11 @@ body="$(mktemp)"
 } > "$body"
 
 # --- 5. open the PR ---
-pr_args=( --slug "$slug" --title "feat: ingest ${slug}" --body-file "$body" )
+pr_args=( --slug "$slug" --title "feat: ingest ${slug}" --body-file "$body" --base "${INGEST_BASE:-main}" )
 [[ -n "$conflict_label" ]] && pr_args+=( --label "$conflict_label" )
 pr_out="$( bash "${SCRIPTS}/open-pr.sh" "${pr_args[@]}" 2>&1 )" && pr_rc=0 || pr_rc=$?
 pr_url="$(printf '%s\n' "$pr_out" | sed -n 's/^PR opened: //p' | head -n1)"
 
-rm -f "$body"
-
 # --- final result line for n8n ---
 jq -nc \
   --arg status   "$([[ $pr_rc -eq 0 ]] && echo ok || echo pr_failed)" \

tests/run-ingest.bats

@@ -132,3 +132,42 @@ EOF
   [[ "$output" == *'"status":"ok"'* ]]
   grep -q 'qwen-test-tag' wiki/log.md
 }
+
+@test "run-ingest: rejects a manifest path that escapes wiki/ (traversal)" {
+  command -v jq >/dev/null 2>&1 || skip "jq not installed"
+  G="$(make_fixture_genome)"; cd "$G"
+  cat > .ingest-manifest.json <<'EOF'
+{ "raw_source":"raw/articles/test.md","reasoning":"r","pr_summary":"s","contradictions":"None",
+  "pages":[{"path":"wiki/../etc/passwd","summary":"x","maturity":"draft","status":"created"}] }
+EOF
+  export KG_LIB_DIR="$LIB_DIR" FORGEJO_URL=http://x FORGEJO_USER=u FORGEJO_TOKEN=t DRY_RUN=1
+  run bash "$SKILL_SCRIPTS/run-ingest.sh" genome-test
+  [ "$status" -ne 0 ]
+  [[ "$output" == *'"status":"error"'* ]]
+}
+
+@test "run-ingest: honours INGEST_BASE for the PR base" {
+  command -v jq >/dev/null 2>&1 || skip "jq not installed"
+  G="$(make_fixture_genome)"; cd "$G"
+  cat > wiki/sources/test-source.md <<'EOF'
+---
+title: "Test Source"
+type: source
+domain: genome-test
+tags: [t]
+maturity: draft
+last_updated: 2026-06-04
+private: false
+---
+body
+EOF
+  cat > .ingest-manifest.json <<'EOF'
+{ "raw_source":"raw/articles/test.md","reasoning":"r","pr_summary":"s","contradictions":"None",
+  "pages":[{"path":"wiki/sources/test-source.md","summary":"s","maturity":"draft","status":"created"}] }
+EOF
+  export KG_LIB_DIR="$LIB_DIR" FORGEJO_URL=http://x FORGEJO_USER=u FORGEJO_TOKEN=t DRY_RUN=1
+  export INGEST_BASE="develop"
+  run bash "$SKILL_SCRIPTS/run-ingest.sh" genome-test
+  [ "$status" -eq 0 ]
+  [[ "$output" == *"develop"* ]]
+}