feat: add linked project field to genome registry

lib/scaffold.sh

@@ -16,17 +16,21 @@ render_template() {
   local content
   content=$(<"$template_file")
 
+  # Defaults (:-) so master-repo templates render even when GENOME_* are unset
+  # (scaffold_master runs before any genome; set -u would otherwise abort here).
   local genome_name_upper
-  genome_name_upper=$(tr '[:lower:]' '[:upper:]' <<< "${GENOME_NAME}")
+  genome_name_upper=$(tr '[:lower:]' '[:upper:]' <<< "${GENOME_NAME:-}")
 
   # Placeholder replacement
-  content="${content//\{\{GENOME_NAME\}\}/${GENOME_NAME}}"
+  content="${content//\{\{GENOME_NAME\}\}/${GENOME_NAME:-}}"
   content="${content//\{\{GENOME_NAME_UPPER\}\}/${genome_name_upper}}"
-  content="${content//\{\{GENOME_DESC\}\}/${GENOME_DESC}}"
+  content="${content//\{\{GENOME_DESC\}\}/${GENOME_DESC:-}}"
-  content="${content//\{\{FORGEJO_URL\}\}/${FORGEJO_URL}}"
+  content="${content//\{\{FORGEJO_URL\}\}/${FORGEJO_URL:-}}"
-  content="${content//\{\{FORGEJO_USER\}\}/${FORGEJO_USER}}"
+  content="${content//\{\{FORGEJO_USER\}\}/${FORGEJO_USER:-}}"
-  content="${content//\{\{VAULTWARDEN_URL\}\}/${VAULTWARDEN_URL}}"
+  content="${content//\{\{VAULTWARDEN_URL\}\}/${VAULTWARDEN_URL:-}}"
-  content="${content//\{\{MASTER_REPO\}\}/${MASTER_REPO}}"
+  content="${content//\{\{MASTER_REPO\}\}/${MASTER_REPO:-}}"
+  # linked project reference (optional) — empty registry field renders as 'none'
+  content="${content//\{\{LINKED_PROJECT\}\}/${GENOME_LINKED:-none}}"
   content="${content//\{\{DATE\}\}/$(date +%Y-%m-%d)}"
 
   mkdir -p "$(dirname "$output_file")"

registry.sh

@@ -19,9 +19,13 @@ LIB_DIR="${PROJECT_ROOT}/lib"
 PROVIDERS_DIR="${PROJECT_ROOT}/providers"
 
 # --- GENOME REGISTRY ---
-# Format: "name|description"
+# Format: "name|description|linked_repo"
+#   - linked_repo is OPTIONAL. Leave empty (trailing pipe) for knowledge-only genomes.
+#   - It is an opaque reference rendered verbatim into the genome's AGENTS.md
+#     (phase-2 project work is parked, so the framework does not act on it yet).
+#   - Example with a project:  "genome-homelab|Keru infrastructure...|keru/homelab-infra"
 GENOMES=(
-  "genome-dev|Web development, TUI, Angular, software architecture"
+  "genome-dev|Web development, TUI, Angular, software architecture|"
-  "genome-finance|Personal finance, investments, market analysis"
+  "genome-finance|Personal finance, investments, market analysis|"
-  "genome-homelab|Keru infrastructure, network configs, architecture logs"
+  "genome-homelab|Keru infrastructure, network configs, architecture logs|"
 )

scripts/add-genome.sh

@@ -11,16 +11,18 @@ source "registry.sh"
 
 GENOME_NAME="${1:-}"
 GENOME_DESC="${2:-}"
+GENOME_LINKED="${3:-}"   # optional: linked project repo reference
 
 if [[ -z "$GENOME_NAME" || -z "$GENOME_DESC" ]]; then
     error "Missing arguments."
-    echo "Usage: $0 <genome-name> <description>"
+    echo "Usage: $0 <genome-name> <description> [linked-repo]"
     exit 1
 fi
 
 step "Adding New Genome: ${GENOME_NAME}"
 
-GENOMES=("${GENOME_NAME}|${GENOME_DESC}")
+# Build a 3-field registry entry (linked_repo may be empty)
+GENOMES=("${GENOME_NAME}|${GENOME_DESC}|${GENOME_LINKED}")
 
 source "scripts/setup-genomes.sh"
 

scripts/setup-genomes.sh

@@ -19,8 +19,9 @@ source "providers/${PROVIDER}.sh"
 step "Processing Genome Registry"
 
 for entry in "${GENOMES[@]}"; do
-    IFS='|' read -r GENOME_NAME GENOME_DESC <<< "$entry"
+    # 3-field format: name|description|linked_repo (linked_repo optional → may be empty)
-    export GENOME_NAME GENOME_DESC
+    IFS='|' read -r GENOME_NAME GENOME_DESC GENOME_LINKED <<< "$entry"
+    export GENOME_NAME GENOME_DESC GENOME_LINKED
 
     info "Processing: ${GENOME_NAME}..."
 

templates/agents-genome.md

@@ -14,12 +14,26 @@
 
 ---
 
+## Linked Project
+
+| Field           | Value                 |
+| --------------- | --------------------- |
+| Project repo    | `{{LINKED_PROJECT}}`  |
+| Branch          | `main`                |
+| Allowed tasks   | `readme, tests, code` |
+| Preferred model | `auto`                |
+
+If `Project repo` is `none`, this genome is knowledge-only — phase-2 project work
+does not apply. When set, after a wiki PR is **merged**, the orchestrator may trigger
+work on this repo within _Allowed tasks_. The agent never touches the project repo
+during ingest.
+
 ## PRIVATE_CONTEXT
 
 **Default: `disabled`** — never infer; require explicit operator declaration per session.
 
 | State      | Behavior                                                                                                                                                                                                                                                                                 |
-|-------|----------|
+| ---------- | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
 | `disabled` | `raw/private/` and `wiki/private/` do not exist. No read, list, grep, or summary on private paths. All outputs safe for collaborators.                                                                                                                                                   |
 | `enabled`  | Operator has confirmed `git-crypt unlock` ran on host. Read/write `private/` authorized. All outputs from private data go exclusively to `wiki/private/`. Prefix every response drawing on private data: `[PRIVATE DATA INCLUDED]`. Never leak private synthesis into public wiki paths. |