skills/ingest/scripts/index-append.py

@@ -18,7 +18,6 @@ import re
 import sys
 
 ENTRY_RE = re.compile(r"^- \[\[")
-LINK_RE = re.compile(r"^- \[\[([^\]]+)\]\]")
 HEADER_RE = re.compile(r"^## ")
 
 
@@ -50,10 +49,6 @@ def main() -> int:
         if fm_open and ln.startswith("last_updated:"):
             lines[i] = f"last_updated: {today}"
 
-    if not fm_open:
-        print("index-append: warning: no frontmatter found, last_updated not bumped",
-              file=sys.stderr)
-
     # 2. Locate the target section [start, end)
     start = None
     for i, ln in enumerate(lines):
@@ -76,31 +71,11 @@ def main() -> int:
     intro = [ln for ln in body if not ENTRY_RE.match(ln)]
     entries = [ln for ln in body if ENTRY_RE.match(ln)]
 
-    # Deduplicate by wikilink PATH, not by exact line: a re-ingest with a changed
-    # summary/maturity should UPDATE the existing entry, not add a duplicate line.
-    new_m = LINK_RE.match(args.entry)
-    new_link = new_m.group(1) if new_m else None
-
-    if new_link is not None:
-        replaced = False
-        for idx, ln in enumerate(entries):
-            m = LINK_RE.match(ln)
-            if m and m.group(1) == new_link:
-                if ln == args.entry:
-                    print("index-append: entry already present, skipping")
-                    return 0
-                entries[idx] = args.entry          # same page, refreshed text
-                replaced = True
-                break
-        if not replaced:
-            entries.append(args.entry)
-    else:
-        # No parseable wikilink — fall back to exact-line dedup.
     if args.entry in entries:
-            print("index-append: entry already present, skipping")
+        print(f"index-append: entry already present, skipping")
         return 0
-        entries.append(args.entry)
 
+    entries.append(args.entry)
     entries.sort(key=str.casefold)
 
     # Normalise intro: drop trailing blanks, keep header + comment(s)

skills/ingest/scripts/log-append.sh

@@ -35,7 +35,7 @@ esac
 
 [[ -f "$LOG_FILE" ]] || { echo "log-append: not found: $LOG_FILE" >&2; exit 1; }
 
-run_id="$(uuidgen 2>/dev/null || cat /proc/sys/kernel/random/uuid 2>/dev/null || python3 -c 'import uuid; print(uuid.uuid4())')"
+run_id="$(uuidgen 2>/dev/null || cat /proc/sys/kernel/random/uuid)"
 today="$(date +%Y-%m-%d)"
 
 {

skills/ingest/scripts/open-pr.sh

@@ -39,13 +39,11 @@ repo="$(basename -s .git "$(git config --get remote.origin.url)")"
 # 1. Branch + commit + push (AGENTS.md rule 5: never commit to main)
 git switch -c "$branch" 2>/dev/null || git switch "$branch"
 git add wiki/
-# Scope BOTH the emptiness check and the commit to wiki/ — never commit anything that
+if git diff --cached --quiet; then
-# happened to be staged outside wiki/ (a stray hook, an aborted prior run, etc.).
-if git diff --cached --quiet -- wiki/; then
   echo "open-pr: nothing staged under wiki/ — aborting" >&2
   exit 1
 fi
-git commit -m "$title" -- wiki/
+git commit -m "$title"
 git push -u origin "$branch"
 
 # DRY_RUN: local git work done; skip the Forgejo API (offline tests).
@@ -55,23 +53,19 @@ if [[ -n "${DRY_RUN:-}" ]]; then
 fi
 
 # 2. Open the PR via Forgejo API (jq builds the JSON safely)
-# TODO: Forgejo-only. When registry.sh/globals.env sets PROVIDER=github, branch on
-# $PROVIDER here and delegate to providers/github.sh (same token + http_code contract).
 body="$(cat "$body_file")"
 payload="$(jq -n --arg head "$branch" --arg base "$base" \
                  --arg title "$title" --arg body "$body" \
                  '{head:$head, base:$base, title:$title, body:$body}')"
 
-resp="$(curl --max-time 30 -s -w '\n%{http_code}' \
+resp="$(curl -s -w '\n%{http_code}' \
   -H "Authorization: token ${FORGEJO_TOKEN}" \
   -H "Content-Type: application/json" \
   -X POST "${FORGEJO_URL}/api/v1/repos/${FORGEJO_USER}/${repo}/pulls" \
   -d "$payload")"
 
-# curl -w appends '\n<code>' AFTER the body, so the code is always the final line and the
+code="$(printf '%s' "$resp" | tail -n1)"
-# body is everything before it. Parameter expansion (no subshells), robust to multi-line JSON.
+json="$(printf '%s' "$resp" | sed '$d')"
-code="${resp##*$'\n'}"
-json="${resp%$'\n'*}"
 
 case "$code" in
   201)
@@ -95,11 +89,11 @@ esac
 
 # 3. Optional label (e.g. CONFLICT). Best-effort; non-fatal.
 if [[ -n "$label" && -n "${number:-}" ]]; then
-  label_id="$(curl --max-time 15 -s -H "Authorization: token ${FORGEJO_TOKEN}" \
+  label_id="$(curl -s -H "Authorization: token ${FORGEJO_TOKEN}" \
     "${FORGEJO_URL}/api/v1/repos/${FORGEJO_USER}/${repo}/labels" \
     | jq -r --arg n "$label" '.[] | select(.name==$n) | .id' | head -n1)"
   if [[ -n "$label_id" && "$label_id" != "null" ]]; then
-    curl --max-time 15 -s -o /dev/null \
+    curl -s -o /dev/null \
       -H "Authorization: token ${FORGEJO_TOKEN}" -H "Content-Type: application/json" \
       -X POST "${FORGEJO_URL}/api/v1/repos/${FORGEJO_USER}/${repo}/issues/${number}/labels" \
       -d "{\"labels\":[${label_id}]}" \

skills/ingest/scripts/run-ingest.sh

@@ -36,7 +36,7 @@ contradictions="$(jq -r '.contradictions // "None"' "$manifest")"
 
 [[ -n "$raw_source" && "$raw_source" != "null" ]] || fail "manifest" "raw_source missing"
 
-slug="$(bash "${SCRIPTS}/slug.sh" "$raw_source")" || fail "slug" "empty or invalid slug for ${raw_source}"
+slug="$(bash "${SCRIPTS}/slug.sh" "$raw_source")"
 
 # --- collect touched paths ---
 mapfile -t created_paths  < <(jq -r '.pages[] | select(.status=="created")  | .path' "$manifest")
@@ -46,11 +46,6 @@ all_paths=( "${created_paths[@]}" "${modified_paths[@]}" )
 
 conflict_label=""
 
-# NOTE: no rollback. Steps below mutate the working tree in order (index → log → commit).
-# All are idempotent on re-run EXCEPT log-append (append-only). If a step fails midway,
-# nothing is committed (open-pr is the only committer) — the operator re-runs, or inspects
-# wiki/ if log-append already wrote a line. The manifest is removed only on full success.
-
 # --- 1. index entries (created pages only), inserted in order ---
 while IFS=$'\t' read -r path summary maturity; do
   [[ -z "$path" ]] && continue
@@ -124,10 +119,4 @@ jq -nc \
   --arg detail   "$pr_out" \
   '{status:$status, slug:$slug, pr_url:$pr_url, lint_clean:$lint_clean, conflict:$conflict, detail:$detail}'
 
-# The manifest is a single file overwritten by each pi run (not accumulating), but on full
+[[ $pr_rc -eq 0 ]]
-# success we remove it so a stale manifest can never be re-processed by mistake.
-if [[ $pr_rc -eq 0 ]]; then
-  rm -f "$manifest"
-else
-  exit 1
-fi

skills/ingest/scripts/scoped-lint.sh

@@ -12,12 +12,7 @@
 # =============================================================================
 set -euo pipefail
 
-: "${KG_LIB_DIR:?set KG_LIB_DIR to the framework lib/ dir (e.g. /opt/knowledge-genome-orchestrator/lib)}"
+: "${KG_LIB_DIR:?set KG_LIB_DIR to the framework lib/ dir (e.g. /opt/knowledge-genome-setup/lib)}"
-
-# Fail clearly if the lib files are missing, rather than a raw `source: No such file`.
-for _f in output.sh lint.sh; do
-  [[ -f "${KG_LIB_DIR}/${_f}" ]] || { echo "scoped-lint: missing ${KG_LIB_DIR}/${_f}" >&2; exit 1; }
-done
 
 # shellcheck source=/dev/null
 source "${KG_LIB_DIR}/output.sh"

skills/ingest/scripts/slug.sh

@@ -13,11 +13,6 @@ input="${1:?usage: slug.sh <path-or-title>}"
 base="${input##*/}"
 base="${base%.*}"
 
-slug="$(printf '%s\n' "$base" \
+printf '%s\n' "$base" \
   | tr '[:upper:]' '[:lower:]' \
-  | sed -E 's/[^a-z0-9]+/-/g; s/-{2,}/-/g; s/^-+//; s/-+$//')"
+  | sed -E 's/[^a-z0-9]+/-/g; s/-{2,}/-/g; s/^-+//; s/-+$//'
-
-# An all-symbols input (e.g. "!!!.md") collapses to "" — refuse rather than emit a
-# broken/empty slug that would produce an invalid branch name downstream.
-[[ -n "$slug" ]] || { echo "slug: empty result for input '${input}'" >&2; exit 1; }
-printf '%s\n' "$slug"

tests/scripts.bats

@@ -51,18 +51,3 @@ load helpers
   python3 "$SKILL_SCRIPTS/index-append.py" --section Sources --entry '- [[sources/dup]] — d. `maturity: draft`'
   [ "$(grep -c 'sources/dup' wiki/index.md)" -eq 1 ]
 }
-
-@test "index-append: updates an existing entry by wikilink path (no duplicate)" {
-  G="$(make_fixture_genome)"; cd "$G"
-  python3 "$SKILL_SCRIPTS/index-append.py" --section Sources --entry '- [[sources/foo]] — old summary. `maturity: draft`'
-  python3 "$SKILL_SCRIPTS/index-append.py" --section Sources --entry '- [[sources/foo]] — new summary. `maturity: stable`'
-  [ "$(grep -c 'sources/foo' wiki/index.md)" -eq 1 ]
-  grep -q 'new summary' wiki/index.md
-  ! grep -q 'old summary' wiki/index.md
-}
-
-@test "slug: refuses an all-symbols input (no empty slug)" {
-  run bash "$SKILL_SCRIPTS/slug.sh" "!!!.md"
-  [ "$status" -ne 0 ]
-  [ -z "$output" ] || [[ "$output" != *"feat/ai-ingest-"* ]]
-}