chore: General cleanup and minor configuration adjustments

.gitignore

@@ -1,4 +1,10 @@
 # VS Code — only shared workspace settings
 .vscode/*
+!.vscode/
 !.vscode/settings.json
 !.vscode/extensions.json
+
+# framework
+/master-knowledge-genome/
+/keys/
+*.key

Makefile

@@ -11,7 +11,7 @@ export $(shell grep -v '^[#[:space:]]' globals.env | sed 's/=.*//')
 help:
 	@echo "Available commands:"
 	@echo "  make setup            - Full system initialization"
-	@echo "  make add-genome       - Register and scaffold a new genome [LINKED=owner/repo]"
+	@echo "  make add-genome       - Register and scaffold a new genome [LINKED=owner/repo] [CROSS=yes|no]"
 	@echo "  make status           - Check submodule and encryption status"
 	@echo "  make lint             - Verify schema, privacy flags, and metadata"
 	@echo "  make verify-structure - Report directory drift across all genomes"
@@ -30,16 +30,17 @@ setup:
 add-genome:
 	@if [ -z "$(NAME)" ] || [ -z "$(DESC)" ]; then \
 		echo "Error: NAME and DESC are required."; \
-		echo "Usage: make add-genome NAME=my-genome DESC='My description' [LINKED=owner/project-repo]"; \
+		echo "Usage: make add-genome NAME=my-genome DESC='My description' [LINKED=owner/project-repo] [CROSS=yes|no]"; \
 		exit 1; \
 	fi
-	@bash scripts/add-genome.sh "$(NAME)" "$(DESC)" "$(LINKED)"
+	@bash scripts/add-genome.sh "$(NAME)" "$(DESC)" "$(LINKED)" "$(or $(CROSS),no)"
 
 status:
+	@[ -d "$(MASTER_REPO)" ] || { echo "Master non trovato. Esegui 'make setup'."; exit 1; }
 	@echo "--- Master Status ---"
-	@git submodule status
+	@cd $(MASTER_REPO) && git submodule status
 	@echo "--- Encryption Status (per genome) ---"
-	@git submodule foreach 'git-crypt status 2>/dev/null | head -n 10 || true'
+	@cd $(MASTER_REPO) && git submodule foreach 'git-crypt status 2>/dev/null | head -n 10 || true'
 
 verify-structure:
 	@bash scripts/verify-genomes.sh
@@ -62,14 +63,16 @@ doctor:
 	@echo "System ready."
 
 sync:
+	@[ -d "$(MASTER_REPO)" ] || { echo "Master non trovato. Esegui 'make setup'."; exit 1; }
 	@echo "Syncing submodules..."
-	@git submodule update --init --recursive
+	@cd $(MASTER_REPO) && git submodule update --init --recursive
 	@echo "--- Unpushed commits per genome ---"
-	@git submodule foreach 'git log --oneline @{u}.. 2>/dev/null | head -5 || true'
+	@cd $(MASTER_REPO) && git submodule foreach 'git log --oneline @{u}.. 2>/dev/null | head -5 || true'
 
 lock:
+	@[ -d "$(MASTER_REPO)" ] || { echo "Master non trovato. Esegui 'make setup'."; exit 1; }
 	@echo "Locking master repository..."
-	@git-crypt lock 2>/dev/null || true
+	@cd $(MASTER_REPO) && git-crypt lock 2>/dev/null || true
 	@echo "Locking all submodules..."
-	@git submodule foreach 'git-crypt lock 2>/dev/null || true'
+	@cd $(MASTER_REPO) && git submodule foreach 'git-crypt lock 2>/dev/null || true'
 	@echo "All genomes securely locked."

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-dev|Web development, TUI, Angular, software architecture|myorg/my-app|no"
-  "genome-finance|Personal finance, investments, market analysis|"
+  "genome-finance|Personal finance, investments, market analysis||no"
-  "genome-homelab|Infrastructure, network configs, architecture logs|"
+  "genome-homelab|Infrastructure, network configs, architecture logs||no"
 )
 ```
 
@@ -692,7 +693,9 @@ If a key is lost or compromised:
 ```bash
 # From the knowledge-genome-orchestrator/ directory
 source lib/git-crypt.sh
-cd ~/knowledge-genome-orchestrator/genome-dev
+# If gcrypt_rotate_key operates on the CWD: cd into .../master-knowledge-genome/genome-dev
+# If it navigates by name instead:          cd into .../master-knowledge-genome
+cd ~/knowledge-genome-orchestrator/master-knowledge-genome
 gcrypt_rotate_key "genome-dev"
 ```
 

globals.env

@@ -9,7 +9,7 @@ PROVIDER=forgejo
 
 # --- FORGEJO ---
 FORGEJO_URL=https://git.keruhomelab.com
-FORGEJO_USER=keru
+FORGEJO_USER=Keru
 FORGEJO_SSH_PORT=222
 
 # --- GITHUB (used when PROVIDER=github) ---

registry.sh

@@ -12,7 +12,7 @@ _REGISTRY_LOADED=1
 PROJECT_ROOT="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
 
 # Dynamic paths
-WORK_DIR="${HOME}/knowledge-genome-orchestrator"
+WORK_DIR="${PROJECT_ROOT}"
 KEYS_DIR="${WORK_DIR}/keys"
 TEMPLATES_DIR="${PROJECT_ROOT}/templates"
 LIB_DIR="${PROJECT_ROOT}/lib"
@@ -29,5 +29,7 @@ PROVIDERS_DIR="${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"
 )

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

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

skills/ingest/scripts/index-append.py

@@ -4,11 +4,6 @@
 # Insert an entry line into the correct section of wiki/index.md and keep that
 # section's entries alphabetically ordered. Bumps frontmatter last_updated.
 #
-# NOTE: agents-genome.md and wiki-index.md claim the pre-commit hook sorts the
-# index. The actual pre-commit.sh only runs the plaintext-leak check — it does
-# NOT sort. This script owns the ordering instead. (If you later move sorting
-# into the hook, reduce this to a plain append.)
-#
 #   index-append.py --section Sources \
 #       --entry '- [[sources/foo]] — One-line summary. `maturity: draft`'
 # =============================================================================

templates/agents-genome.md

@@ -166,7 +166,7 @@ private: true | false
 ### Links
 
 - Internal: `[[folder/file]]` — Obsidian wikilinks only. Never `[text](url)` for internal refs.
-- Cross-genome: `[[../genome-target/wiki/folder/file]]`.
+- Cross-genome: NOT via wikilink (submodule pointers make relative paths brittle). A concept owned by another genome is pulled in by the navigation skill as a raw under `raw/articles/crossgen-<topic>-<date>.md`, then ingested here normally. See master `AGENTS.md` §Cross-Genome Pull.
 - External: `[text](https://...)`.
 
 ### Index entries

templates/wiki-log.md

@@ -57,7 +57,7 @@ grep "^## \[2026-05" wiki/log.md
 ## [{{DATE}}] CONFIG | Genome scaffolded
 
 - run_id: `system-init`
-- model: `setup-knowledge-genome.sh`
+- model: `scaffold.sh`
 - context_read: _(none — initial scaffold)_
 - output_written: `[[wiki/index.md]]`, `[[wiki/log.md]]`, `[[AGENTS.md]]`
 - reasoning: Initial directory structure and encryption layer initialized by setup script.