docs: Add developer notes on code smells and design tradeoffs

lib/structure.sh

@@ -9,6 +9,14 @@
 # structure check can never drift apart.
 # =============================================================================
 
+# NOTE — Return-code smell
+# Several functions in this file (and in lint.sh) use the return code as a
+# numeric counter (e.g. return $missing). This is a known smell: exit codes
+# wrap at 256 and conflate "count of problems" with "exit status". At the
+# current scale (<10 problems per run) the wrap-around risk is zero, so we
+# accept it pragmatically. If counts ever grow, switch to stdout counters
+# or dedicated global variables.
+
 # Canonical directories every genome must have.
 # raw/* are input buckets (collaborator-writable); wiki/* is the agent-owned,
 # contract-bound layout the lint, the index sections and the ingest skill depend on.
@@ -43,6 +51,7 @@ structure_report() {
     info "extra (not in canon): ${d}"
   done < <(find "${base}/raw" "${base}/wiki" -mindepth 1 -type d 2>/dev/null)
 
+  # NOTE: return $missing is a smell — see header. Kept for compatibility.
   return $missing
 }
 

scripts/add-genome.sh

@@ -24,6 +24,15 @@ step "Adding New Genome: ${GENOME_NAME}"
 # Build a 3-field registry entry (linked_repo may be empty)
 GENOMES=("${GENOME_NAME}|${GENOME_DESC}|${GENOME_LINKED}")
 
+# NOTE — Maintenance smell
+# We source setup-genomes.sh as a library/orchestrator hybrid. This works because:
+#   - registry.sh is guarded against double-source (idempotent guard)
+#   - setup-genomes.sh checks WORK_DIR before re-sourcing registry.sh
+#   - GENOMES is built locally just before the source, so it is not clobbered
+# However, sourcing an orchestration script as a library makes the control flow
+# harder to trace. If this grows, refactor into a shared function (e.g. setup_one_genome)
+# called by both add-genome.sh and setup-genomes.sh.
+
 source "scripts/setup-genomes.sh"
 
 success "Genome '${GENOME_NAME}' added and linked successfully!"

skills/ingest/scripts/run-ingest.sh

@@ -59,10 +59,14 @@ 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.
+# NOTE: No rollback. The steps below modify the working tree in order (index → log → commit).
+# All steps 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 checks
+# wiki/ if log-append has already written a line. The manifest is removed only upon full success.
+# log-append is not idempotent: a re-run after a post-log failure produces
+# duplicate lines. This is accepted by design (append-only ledger, no rollback). If this
+# becomes a nuisance tomorrow, add a dedup check on run_id in log-append.sh
+# (grep for run_id before appending). Manual recovery: grep for run_id in wiki/log.md.
 
 # --- 1. index entries (created pages only), inserted in order ---
 while IFS=$'\t' read -r path summary maturity; do