From 7f10a4f77097552c4fa5c0787f6e2e7b4c6f936a Mon Sep 17 00:00:00 2001
From: Matteo Cherubini <cherubinimatte@gmail.com>
Date: Sat, 9 May 2026 17:25:36 +0200
Subject: [PATCH] refactor: Split configuration into `globals.env` and
 `registry.sh`

---
 scripts/add-genome.sh    | 5 ++---
 scripts/lint-genomes.sh  | 5 +++--
 scripts/setup-genomes.sh | 8 ++++++--
 scripts/setup-master.sh  | 3 ++-
 scripts/setup.sh         | 5 +++--
 5 files changed, 16 insertions(+), 10 deletions(-)

diff --git a/scripts/add-genome.sh b/scripts/add-genome.sh
index fc69296..37dab87 100644
--- a/scripts/add-genome.sh
+++ b/scripts/add-genome.sh
@@ -6,7 +6,8 @@
 
 set -euo pipefail
 source "lib/output.sh"
-source "config.env"
+source "globals.env"
+source "registry.sh"
 
 GENOME_NAME="${1:-}"
 GENOME_DESC="${2:-}"
@@ -19,10 +20,8 @@ fi
 
 step "Adding New Genome: ${GENOME_NAME}"
 
-# Sovrascrivo l'array per la sessione corrente
 GENOMES=("${GENOME_NAME}|${GENOME_DESC}")
 
-# FIX BUG 2: Uso source invece di bash per mantenere il context dell'array
 source "scripts/setup-genomes.sh"
 
 success "Genome '${GENOME_NAME}' added and linked successfully!"
diff --git a/scripts/lint-genomes.sh b/scripts/lint-genomes.sh
index 392fac7..7c2a77e 100644
--- a/scripts/lint-genomes.sh
+++ b/scripts/lint-genomes.sh
@@ -2,13 +2,14 @@
 # =============================================================================
 # scripts/lint-genomes.sh
 # Executes quality control across all registered genomes.
-# Iterates from the GENOMES registry in config.env — not from filesystem patterns —
+# Iterates from the GENOMES registry in registry.sh — not from filesystem patterns —
 # so all genomes are covered regardless of their naming convention.
 # =============================================================================
 
 set -euo pipefail
 source "lib/output.sh"
-source "config.env"
+source "globals.env"
+source "registry.sh"
 source "lib/lint.sh"
 
 step "Starting Knowledge Genome Linting"
diff --git a/scripts/setup-genomes.sh b/scripts/setup-genomes.sh
index 1add46a..b8a7863 100644
--- a/scripts/setup-genomes.sh
+++ b/scripts/setup-genomes.sh
@@ -6,7 +6,12 @@
 
 set -euo pipefail
 source "lib/output.sh"
-source "config.env"
+source "globals.env"
+
+if [[ -z "${WORK_DIR:-}" ]]; then
+    source "registry.sh"
+fi
+
 source "lib/scaffold.sh"
 source "lib/git-crypt.sh"
 source "providers/${PROVIDER}.sh"
@@ -29,7 +34,6 @@ for entry in "${GENOMES[@]}"; do
         cd "${WORK_DIR}/${MASTER_REPO}"
         info "Linking ${GENOME_NAME} as a submodule..."
 
-        # FIX BUG 1: Adding the submodule clones the empty remote repository
         git submodule add "${SSH_URL}" "${GENOME_NAME}"
 
         cd "${GENOME_NAME}"
diff --git a/scripts/setup-master.sh b/scripts/setup-master.sh
index 4707f5b..42c3e1a 100644
--- a/scripts/setup-master.sh
+++ b/scripts/setup-master.sh
@@ -6,7 +6,8 @@
 
 set -euo pipefail
 source "lib/output.sh"
-source "config.env"
+source "globals.env"
+source "registry.sh"
 source "lib/scaffold.sh"
 source "providers/${PROVIDER}.sh" # Required for remote creation
 
diff --git a/scripts/setup.sh b/scripts/setup.sh
index eb2e5b7..0bc3107 100644
--- a/scripts/setup.sh
+++ b/scripts/setup.sh
@@ -10,7 +10,8 @@ set -euo pipefail
 # Resolve script directory and source core components
 SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")/.." && pwd)"
 source "${SCRIPT_DIR}/lib/output.sh"
-source "${SCRIPT_DIR}/config.env"
+source "${SCRIPT_DIR}/globals.env"
+source "${SCRIPT_DIR}/registry.sh"
 source "${SCRIPT_DIR}/lib/deps.sh"
 
 step "Starting Knowledge Genome Setup"
@@ -24,7 +25,7 @@ check_git_identity
 info "Initializing Master Repository..."
 bash "${SCRIPT_DIR}/scripts/setup-master.sh"
 
-# 3. Genomes Provisioning (as defined in config.env)
+# 3. Genomes Provisioning (as defined in registry.sh)
 info "Provisioning registered Genomes..."
 bash "${SCRIPT_DIR}/scripts/setup-genomes.sh"