feature: Add pi orphan-wiki command to detect unlinked pages

deploy/vm101/n8n-pi-wrap

@@ -11,6 +11,13 @@ case "$cmd" in
     # lines 54/59), so pending-raw.sh resolves its sibling slug.sh via BASH_SOURCE.
     exec "${HOME}/.pi/agent/skills/ingest/scripts/pending-raw.sh" "$genome"
     ;;
+  "pi orphan-wiki "*)
+    genome="${cmd#pi orphan-wiki }"
+    case "$genome" in ""|*[!a-z0-9-]*) echo '{"status":"error","reason":"invalid genome name"}'; exit 1;; esac
+    logger -t n8n-pi-wrap "ok: pi orphan-wiki ${genome}"
+    set -a; . "${HOME}/.config/knowledge-genome.env" 2>/dev/null || true; set +a
+    exec "${HOME}/.pi/agent/skills/ingest/scripts/orphan-wiki.sh" "$genome"
+    ;;
  "pi run")
    logger -t n8n-pi-wrap "ok: pi run (prompt via stdin)"
    prompt=$(cat)

skills/ingest/scripts/orphan-wiki.sh

@@ -0,0 +1,35 @@
+#!/usr/bin/env bash
+# =============================================================================
+# orphan-wiki.sh — find source pages whose raw source no longer exists.
+# Reads source_path from each wiki/sources/*.md frontmatter. If the raw is gone,
+# the page is orphaned. Emits JSON envelope: {status, genome, count, files[], detail[]}.
+# Read-only: no lock needed (same policy as pending-raw).
+# =============================================================================
+set -euo pipefail
+
+genome="${1:?usage: orphan-wiki.sh <genome>}"
+base_dir="${GENOMES_ROOT:-${HOME}/genomes}"
+cd "${base_dir}/${genome}" 2>/dev/null || { echo '{"status":"error","reason":"unknown genome"}'; exit 1; }
+
+# Clean start on the configured base (single source of truth in lib/clean-start.sh).
+: "${KG_LIB_DIR:=${HOME}/knowledge-genome-orchestrator/lib}"
+source "${KG_LIB_DIR}/clean-start.sh" 2>/dev/null \
+  || { echo '{"status":"error","reason":"clean-start.sh not found"}'; exit 1; }
+clean_start || { echo '{"status":"error","reason":"clean-start failed"}'; exit 1; }
+
+declare -a ORPH=()
+for page in wiki/sources/*.md; do
+  [[ -e "$page" ]] || continue
+  sp="$(sed -n 's/^source_path:[[:space:]]*//p' "$page" | tr -d '\r' | head -n1)"
+  # Pages without source_path are pre-Step-2 legacy: ignore, don't false-positive.
+  [[ -n "$sp" ]] || continue
+  [[ -f "$sp" ]] || ORPH+=("$page")
+done
+
+if [[ ${#ORPH[@]} -eq 0 ]]; then
+  echo '{"status":"ok","genome":"'"$genome"'","count":0,"files":[],"detail":[]}'
+else
+  for x in "${ORPH[@]}"; do printf '%s\torphan\n' "$x"; done \
+    | jq -R 'split("\t") | {path: .[0], reason: .[1]}' \
+    | jq -s --arg g "$genome" '{status:"ok", genome:$g, count:length, files:[.[].path], detail:.}'
+fi

tests/orphan-wiki.bats

@@ -0,0 +1,38 @@
+#!/usr/bin/env bats
+setup() {
+  load 'helpers'
+  export ORPHAN="${SKILL_SCRIPTS}/orphan-wiki.sh"
+  export GENOMES_ROOT="${BATS_TEST_TMPDIR}"
+  export INGEST_BASE="main"
+  export KG_LIB_DIR="${LIB_DIR}"            # orphan-wiki.sh sources clean-start.sh via KG_LIB_DIR
+  g_src="$(make_fixture_genome)"
+  export g_name="fixture-genome"
+  mv "$g_src" "${GENOMES_ROOT}/${g_name}"
+  export g="${GENOMES_ROOT}/${g_name}"
+  ( cd "$g" && rm -f raw/articles/test.md && git add -A && git commit -q -m "clear" && git push -q )
+}
+@test "orphan-wiki: no orphans when raw and source page match" {
+  mkdir -p "${g}/raw/articles"; echo "content" > "${g}/raw/articles/existing.md"
+  hash="$(sha256sum "${g}/raw/articles/existing.md" | cut -d' ' -f1)"
+  mkdir -p "${g}/wiki/sources"
+  printf -- '---\nsource_path: raw/articles/existing.md\nsource_sha256: %s\n---\n' "$hash" > "${g}/wiki/sources/existing.md"
+  ( cd "$g" && git add . && git commit -q -m "setup" && git push -q )
+  run bash "$ORPHAN" "$g_name"
+  [ "$status" -eq 0 ]; echo "$output" | jq -e '.count == 0'
+}
+@test "orphan-wiki: detects orphaned source page" {
+  mkdir -p "${g}/wiki/sources"
+  printf -- '---\nsource_path: raw/articles/deleted.md\nsource_sha256: abc123\n---\n' > "${g}/wiki/sources/orphaned.md"
+  ( cd "$g" && git add . && git commit -q -m "orphan" && git push -q )
+  run bash "$ORPHAN" "$g_name"
+  [ "$status" -eq 0 ]
+  echo "$output" | jq -e '.count == 1'
+  echo "$output" | jq -e '.detail[0].reason == "orphan"'
+}
+@test "orphan-wiki: ignores legacy pages without source_path" {
+  mkdir -p "${g}/wiki/sources"
+  printf -- '---\ntitle: "Legacy"\ntype: source\n---\n' > "${g}/wiki/sources/legacy.md"
+  ( cd "$g" && git add . && git commit -q -m "legacy" && git push -q )
+  run bash "$ORPHAN" "$g_name"
+  [ "$status" -eq 0 ]; echo "$output" | jq -e '.count == 0'
+}

tests/permissions.bats

@@ -18,6 +18,7 @@ EXECUTABLES=(
   skills/ingest/scripts/log-append.sh
   skills/ingest/scripts/slug.sh
   skills/ingest/scripts/pending-raw.sh
+  skills/ingest/scripts/orphan-wiki.sh
   skills/ingest/scripts/index-append.py
   scripts/add-genome.sh
   scripts/setup.sh