From 6558ee486af6a0ab799b7b53aa5020c6f378f8e7 Mon Sep 17 00:00:00 2001
From: Matteo Cherubini <cherubinimatte@gmail.com>
Date: Fri, 12 Jun 2026 10:49:04 +0200
Subject: [PATCH] feat: Add 'cross_source' property to genome registry

---
 Makefile                  | 2 +-
 README.md                 | 9 +++++----
 registry.sh               | 4 +++-
 scripts/setup-genomes.sh  | 2 +-
 scripts/verify-genomes.sh | 2 +-
 5 files changed, 11 insertions(+), 8 deletions(-)

diff --git a/Makefile b/Makefile
index cfd4537..527fd48 100644
--- a/Makefile
+++ b/Makefile
@@ -11,7 +11,7 @@ export $(shell grep -v '^[#[:space:]]' globals.env | sed 's/=.*//')
 help:
 	@echo "Available commands:"
 	@echo "  make setup            - Full system initialization"
-	@echo "  make add-genome       - Register and scaffold a new genome [LINKED=owner/repo]"
+	@echo "  make add-genome       - Register and scaffold a new genome [LINKED=owner/repo] [CROSS=yes|no]"
 	@echo "  make status           - Check submodule and encryption status"
 	@echo "  make lint             - Verify schema, privacy flags, and metadata"
 	@echo "  make verify-structure - Report directory drift across all genomes"
diff --git a/README.md b/README.md
index f682de4..d5d16d3 100644
--- a/README.md
+++ b/README.md
@@ -330,13 +330,14 @@ WORK_DIR="${HOME}/knowledge-genome-orchestrator"
 KEYS_DIR="${WORK_DIR}/keys"
 
 # Genome registry — format: "name|description|linked_repo"
-# The third field is OPTIONAL:
+# The third and fourth fields are OPTIONAL:
 #   - leave it empty  → knowledge-only genome (no linked project)
 #   - owner/repo      → genome is linked to that project repository (rendered into AGENTS.md)
+#   - cross_source    → yes|no (default no): whether the cross-genome collector may read this genome as a source
 GENOMES=(
-  "genome-dev|Web development, TUI, Angular, software architecture|myorg/my-app"
-  "genome-finance|Personal finance, investments, market analysis|"
-  "genome-homelab|Infrastructure, network configs, architecture logs|"
+  "genome-dev|Web development, TUI, Angular, software architecture|myorg/my-app|no"
+  "genome-finance|Personal finance, investments, market analysis||no"
+  "genome-homelab|Infrastructure, network configs, architecture logs||no"
 )
 ```
 
diff --git a/registry.sh b/registry.sh
index 3083cad..1d0df3f 100644
--- a/registry.sh
+++ b/registry.sh
@@ -29,5 +29,7 @@ PROVIDERS_DIR="${PROJECT_ROOT}/providers"
 # Example: "genome-work|Work notes and architecture logs||no"
 #          "genome-finance|Personal finance|user/repo-finance|no"
 GENOMES=(
-  "genome-example|Template genome description for knowledge management||no"
+  # Disposable sandbox: exercise the full pipeline (ingest -> PR) end-to-end.
+  # Created by `make setup`. Replace with real domains once the circle is validated.
+  "genome-test|Disposable sandbox for pipeline testing||no"
 )
diff --git a/scripts/setup-genomes.sh b/scripts/setup-genomes.sh
index f3aa6cd..1617200 100644
--- a/scripts/setup-genomes.sh
+++ b/scripts/setup-genomes.sh
@@ -19,7 +19,7 @@ source "providers/${PROVIDER}.sh"
 step "Processing Genome Registry"
 
 for entry in "${GENOMES[@]}"; do
-    # 3-field format: name|description|linked_repo (linked_repo optional → may be empty)
+    # 4-field format: name|description|linked_repo|cross_source linked_repo optional (may be empty); cross_source defaults to "no".
     IFS='|' read -r GENOME_NAME GENOME_DESC GENOME_LINKED GENOME_CROSS_SOURCE <<< "$entry"
     GENOME_CROSS_SOURCE="${GENOME_CROSS_SOURCE:-no}"
     export GENOME_NAME GENOME_DESC GENOME_LINKED GENOME_CROSS_SOURCE
diff --git a/scripts/verify-genomes.sh b/scripts/verify-genomes.sh
index 85a4a62..fc5ed19 100644
--- a/scripts/verify-genomes.sh
+++ b/scripts/verify-genomes.sh
@@ -22,7 +22,7 @@ step "Genome structure: ${MODE}"
 
 TOTAL_MISSING=0
 for entry in "${GENOMES[@]}"; do
-  IFS='|' read -r GENOME_NAME _ _ <<< "$entry"     # 3-field registry; ignore desc + linked
+  IFS='|' read -r GENOME_NAME _ <<< "$entry"       # 4-field registry; only GENOME_NAME used here
   genome_dir="${WORK_DIR}/${MASTER_REPO}/${GENOME_NAME}"
 
   if [[ ! -d "$genome_dir" ]]; then