refactor: Improve script loading and project root resolution

registry.sh

@@ -1,17 +1,22 @@
 #!/usr/bin/env bash
 # =============================================================================
-# registry.sh
-# Bash-only runtime config: dynamic paths and genome registry array.
-# Source this in shell scripts — never included by Make or env parsers.
+# registry.sh - Knowledge Genome Registry
+# Dynamic paths and genome definitions.
 # =============================================================================
 
-# Dynamic paths — resolved relative to this file at source time
-SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
+# Guard against double sourcing
+[[ -n "${_REGISTRY_LOADED:-}" ]] && return
+_REGISTRY_LOADED=1
+
+# Resolve project root relative to this file
+PROJECT_ROOT="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
+
+# Dynamic paths
 WORK_DIR="${HOME}/knowledge-genome-setup"
 KEYS_DIR="${WORK_DIR}/keys"
-TEMPLATES_DIR="${SCRIPT_DIR}/templates"
-LIB_DIR="${SCRIPT_DIR}/lib"
-PROVIDERS_DIR="${SCRIPT_DIR}/providers"
+TEMPLATES_DIR="${PROJECT_ROOT}/templates"
+LIB_DIR="${PROJECT_ROOT}/lib"
+PROVIDERS_DIR="${PROJECT_ROOT}/providers"
 
 # --- GENOME REGISTRY ---
 # Format: "name|description"

scripts/setup.sh

@@ -9,6 +9,7 @@ set -euo pipefail
 
 # Resolve script directory and source core components
 SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")/.." && pwd)"
+cd "${SCRIPT_DIR}"   # All child scripts use relative paths from project root
 source "${SCRIPT_DIR}/lib/output.sh"
 source "${SCRIPT_DIR}/globals.env"
 source "${SCRIPT_DIR}/registry.sh"