Refactor setup workflow

Bins/versions.json

@@ -0,0 +1,32 @@
+{
+	"nvim": {
+		"owner": "neovim",
+		"repo": "neovim",
+		"version": "v0.11.5",
+		"linux": {
+			"x86_64": {
+				"asset": "nvim-linux-x86_64.tar.gz",
+				"binary": "nvim-linux-x86_64/bin/nvim"
+			},
+			"aarch64": {
+				"asset": "nvim-linux-arm64.tar.gz",
+				"binary": "nvim-linux-arm64/bin/nvim"
+			}
+		}
+	},
+	"eza": {
+		"owner": "eza-community",
+		"repo": "eza",
+		"version": "v0.23.4",
+		"linux": {
+			"x86_64": {
+				"asset": "eza_x86_64-unknown-linux-gnu.tar.gz",
+				"binary": "eza"
+			},
+			"aarch64": {
+				"asset": "eza_aarch64-unknown-linux-gnu.tar.gz",
+				"binary": "eza"
+			}
+		}
+	}
+}

Commands/Bin/mod.just

@@ -0,0 +1,22 @@
+project_root := justfile_directory()
+bin_script_dir := project_root + "/Scripts/bin"
+
+# Install all pinned repo-managed binaries into ~/.local/bin.
+install-all:
+    bash '{{bin_script_dir}}/install.sh' --all
+
+# Install one pinned repo-managed binary into ~/.local/bin.
+install tool:
+    bash '{{bin_script_dir}}/install.sh' '{{tool}}'
+
+# Update the pinned version for a binary. If no version is given, open an fzf selector when available.
+update tool version='':
+    bash '{{bin_script_dir}}/update.sh' '{{tool}}' '{{version}}'
+
+# List available releases for a supported binary.
+list tool:
+    bash '{{bin_script_dir}}/update.sh' --list '{{tool}}'
+
+# Print the currently pinned versions.
+show:
+    cat '{{project_root}}/Bins/versions.json'

Commands/Lang/mod.just

@@ -0,0 +1,20 @@
+project_root := justfile_directory()
+scripts_dir := project_root + "/Scripts"
+
+node:
+    bash '{{scripts_dir}}/node.sh'
+
+go:
+    bash '{{scripts_dir}}/go.sh'
+
+rust:
+    bash '{{scripts_dir}}/rust.sh'
+
+python:
+    bash '{{scripts_dir}}/python.sh'
+
+r:
+    bash '{{scripts_dir}}/r.sh'
+
+cpp:
+    bash '{{scripts_dir}}/cpp.sh'

Commands/Setup/mod.just

@@ -0,0 +1,43 @@
+project_root := justfile_directory()
+scripts_dir := project_root + "/Scripts"
+
+# Run the full setup flow.
+all:
+    bash '{{scripts_dir}}/setup.sh'
+
+# Install the base system layer only.
+base:
+    bash '{{scripts_dir}}/base.sh'
+
+# Stow shell files into $HOME.
+stow:
+    stow --dir='{{project_root}}' Zsh --target="$HOME"
+
+# Remove stowed shell files from $HOME.
+clean:
+    stow --dir='{{project_root}}' -D Zsh --target="$HOME"
+
+# Pull latest changes and rerun setup.
+update:
+    git -C '{{project_root}}' pull origin main
+    just --justfile '{{project_root}}/Justfile' setup all
+
+# Run distro test containers.
+test-ubuntu:
+    echo "Ubuntu Test"
+    docker run -it --rm -e TERM=xterm-256color -v '{{project_root}}':/root/dotfiles ubuntu:latest \
+        bash -c "export DEBIAN_FRONTEND=noninteractive && \
+        apt-get update && \
+        apt-get install -y sudo git make curl && \
+        cd /root/dotfiles && \
+        make setup"
+
+test-arch:
+    echo "Spawning Arch Container..."
+    docker run -it --rm -e TERM=xterm-256color -v '{{project_root}}':/root/dotfiles archlinux:latest \
+        bash -c "pacman -Sy --noconfirm base-devel git make sudo && cd /root/dotfiles && make setup"
+
+test-fedora:
+    echo "Spawning Fedora Container..."
+    docker run -it --rm -e TERM=xterm-256color -v '{{project_root}}':/root/dotfiles fedora:latest \
+        bash -c "dnf install -y git make sudo curl which passwd procps-ng && cd /root/dotfiles && make setup"

Justfile

@@ -0,0 +1,9 @@
+set shell := ["bash", "-cu"]
+
+mod bin "Commands/Bin"
+mod lang "Commands/Lang"
+mod setup "Commands/Setup"
+
+[default]
+help:
+    just --list --list-submodules

Makefile

@@ -1,93 +1,10 @@
 # Makefile
 
-REBOOT_MARKER := .setup-reboot-required
+SCRIPTS_DIR := ./Scripts
 
 # Default target
-all: stow
+all: setup
 
-# Full Setup
+# Bootstrap entrypoint for first-run setup.
 setup:
-	@set -e; \
+	bash $(SCRIPTS_DIR)/setup.sh
-	rm -f $(REBOOT_MARKER); \
-	bash ./scripts/base.sh; \
-	if [ -f $(REBOOT_MARKER) ]; then \
-		rm -f $(REBOOT_MARKER); \
-		echo "Package layering finished. Reboot, then rerun make setup."; \
-		exit 0; \
-	fi; \
-	bash ./scripts/node.sh; \
-	bash ./scripts/go.sh; \
-	bash ./scripts/rust.sh; \
-	bash ./scripts/python.sh; \
-	if [ -f $(REBOOT_MARKER) ]; then \
-		rm -f $(REBOOT_MARKER); \
-		echo "Package layering finished. Reboot, then rerun make setup."; \
-		exit 0; \
-	fi; \
-	bash ./scripts/r.sh; \
-	if [ -f $(REBOOT_MARKER) ]; then \
-		rm -f $(REBOOT_MARKER); \
-		echo "Package layering finished. Reboot, then rerun make setup."; \
-		exit 0; \
-	fi; \
-	$(MAKE) clean; \
-	$(MAKE) stow; \
-	echo "Full setup completed."
-
-base:
-	bash ./scripts/base.sh
-	@echo "Base setup completed."
-
-# Just stow the dotfiles
-stow:
-	stow . --target=$$HOME --ignore=".git" --ignore=".gitignore" --ignore="README.md" --ignore=".zsh_secrets" --ignore=".zsh_secrets.example" --ignore="LICENSE" --ignore="Makefile" --ignore="bin" --ignore="scripts"
-	@echo "Dotfiles linked."
-
-# Clean old files and links
-clean:
-	stow -D . --target=$$HOME
-	@echo "Links removed."
-
-# Pull Git Updates
-update:
-	git pull origin main
-	$(MAKE) setup
-
-# Language Setups
-node:
-	bash ./scripts/node.sh
-
-go:
-	bash ./scripts/go.sh
-
-rust:
-	bash ./scripts/rust.sh
-
-python:
-	bash ./scripts/python.sh
-
-r:
-	bash ./scripts/r.sh
-
-cpp:
-	bash ./scripts/cpp.sh
-
-# Docker Tests
-test-ubuntu:
-	@echo "Ubuntu Test"
-	docker run -it --rm -e TERM=xterm-256color -v $(PWD):/root/dotfiles ubuntu:latest \
-	bash -c "export DEBIAN_FRONTEND=noninteractive && \
-	apt-get update && \
-	apt-get install -y sudo git make curl && \
-	cd /root/dotfiles && \
-	make setup"
-
-test-arch:
-	@echo "Spawning Arch Container..."
-	docker run -it --rm -e TERM=xterm-256color -v $(PWD):/root/dotfiles archlinux:latest \
-	bash -c "pacman -Sy --noconfirm base-devel git make sudo && cd /root/dotfiles && make setup"
-
-test-fedora:
-	@echo "Spawning Fedora Container..."
-	docker run -it --rm -e TERM=xterm-256color -v $(PWD):/root/dotfiles fedora:latest \
-	bash -c "dnf install -y git make sudo curl which passwd procps-ng && cd /root/dotfiles && make setup"

Scripts/base.sh

@@ -1,6 +1,6 @@
 #!/bin/bash
 
-# Path: scripts/base.sh
+# Path: Scripts/base.sh
 
 set -e
 
@@ -154,10 +154,8 @@ if is_debian_family || is_fedora_family; then
     [ -f /usr/bin/batcat ] && sudo ln -sf /usr/bin/batcat /usr/local/bin/bat
 fi
 
-# Moving Pre-Built bin to .local/bin
+# Installing pinned repo-managed CLI binaries
-mkdir -p "$HOME/.local/bin"
+bash "$REPO_ROOT/Scripts/bin/install.sh" --all
-cp -f "$REPO_ROOT/bin/"* "$HOME/.local/bin/"
-chmod +x "$HOME/.local/bin/"*
 
 if ! command -v rclone &> /dev/null; then
     echo -e "${BLUE}    LOG:${YELLOW} Installing Rclone CLI...${NC}"
@@ -250,7 +248,8 @@ fi
 
 # 6. Cleanup & Secrets
 rm -f "$HOME/.zshrc" "$HOME/.zsh_aliases"
-touch "$HOME/.zsh_secrets"
+mkdir -p "$REPO_ROOT/Zsh"
+touch "$REPO_ROOT/Zsh/.zsh_secrets"
 
 # 7. Set Shell
 TARGET_SHELL="$(command -v zsh)"

Scripts/bin/install.sh

@@ -0,0 +1,99 @@
+#!/bin/bash
+
+set -euo pipefail
+
+SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
+REPO_ROOT="$(dirname "$(dirname "$SCRIPT_DIR")")"
+MANIFEST="$REPO_ROOT/Bins/versions.json"
+TARGET_DIR="$HOME/.local/bin"
+
+ensure_deps() {
+    local missing=()
+
+    for cmd in jq curl tar; do
+        if ! command -v "$cmd" >/dev/null 2>&1; then
+            missing+=("$cmd")
+        fi
+    done
+
+    if [ "${#missing[@]}" -gt 0 ]; then
+        printf 'Missing required commands: %s\n' "${missing[*]}" >&2
+        exit 1
+    fi
+}
+
+detect_arch() {
+    case "$(uname -m)" in
+        x86_64) printf 'x86_64\n' ;;
+        aarch64|arm64) printf 'aarch64\n' ;;
+        *)
+            printf 'Unsupported architecture: %s\n' "$(uname -m)" >&2
+            exit 1
+            ;;
+    esac
+}
+
+install_tool() {
+    local tool="$1"
+    local arch version owner repo asset binary_rel url tmp_dir archive_path extracted_path target_path
+
+    arch="$(detect_arch)"
+
+    if ! jq -e --arg tool "$tool" '.[$tool]' "$MANIFEST" >/dev/null; then
+        printf 'Unsupported tool: %s\n' "$tool" >&2
+        exit 1
+    fi
+
+    version="$(jq -r --arg tool "$tool" '.[$tool].version' "$MANIFEST")"
+    owner="$(jq -r --arg tool "$tool" '.[$tool].owner' "$MANIFEST")"
+    repo="$(jq -r --arg tool "$tool" '.[$tool].repo' "$MANIFEST")"
+    asset="$(jq -r --arg tool "$tool" --arg arch "$arch" '.[$tool].linux[$arch].asset' "$MANIFEST")"
+    binary_rel="$(jq -r --arg tool "$tool" --arg arch "$arch" '.[$tool].linux[$arch].binary' "$MANIFEST")"
+
+    if [ -z "$asset" ] || [ "$asset" = "null" ] || [ -z "$binary_rel" ] || [ "$binary_rel" = "null" ]; then
+        printf 'No Linux asset mapping for %s on %s\n' "$tool" "$arch" >&2
+        exit 1
+    fi
+
+    mkdir -p "$TARGET_DIR"
+    tmp_dir="$(mktemp -d)"
+    archive_path="$tmp_dir/$asset"
+    url="https://github.com/$owner/$repo/releases/download/$version/$asset"
+
+    printf 'Installing %s %s\n' "$tool" "$version"
+    curl -fL "$url" -o "$archive_path"
+    tar -xzf "$archive_path" -C "$tmp_dir"
+
+    extracted_path="$tmp_dir/$binary_rel"
+    if [ ! -f "$extracted_path" ]; then
+        printf 'Expected binary not found after extraction: %s\n' "$binary_rel" >&2
+        rm -rf "$tmp_dir"
+        exit 1
+    fi
+
+    target_path="$TARGET_DIR/$tool"
+    install -m 755 "$extracted_path" "$target_path"
+    rm -rf "$tmp_dir"
+
+    printf 'Installed %s -> %s\n' "$tool" "$target_path"
+}
+
+main() {
+    ensure_deps
+
+    if [ "${1:-}" = "--all" ]; then
+        while IFS= read -r tool; do
+            install_tool "$tool"
+        done < <(jq -r 'keys[]' "$MANIFEST")
+        exit 0
+    fi
+
+    if [ -z "${1:-}" ]; then
+        printf 'Usage: %s [--all|tool]\n' "$0" >&2
+        exit 1
+    fi
+
+    install_tool "$1"
+}
+
+main "$@"

Scripts/bin/update.sh

@@ -0,0 +1,135 @@
+#!/bin/bash
+
+set -euo pipefail
+
+SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
+REPO_ROOT="$(dirname "$(dirname "$SCRIPT_DIR")")"
+MANIFEST="$REPO_ROOT/Bins/versions.json"
+
+ensure_deps() {
+    local missing=()
+
+    for cmd in jq curl python3; do
+        if ! command -v "$cmd" >/dev/null 2>&1; then
+            missing+=("$cmd")
+        fi
+    done
+
+    if [ "${#missing[@]}" -gt 0 ]; then
+        printf 'Missing required commands: %s\n' "${missing[*]}" >&2
+        exit 1
+    fi
+}
+
+github_api() {
+    local path="$1"
+    local auth_args=()
+
+    if [ -n "${GITHUB_TOKEN:-}" ]; then
+        auth_args=(-H "Authorization: Bearer $GITHUB_TOKEN")
+    fi
+
+    curl -fsSL \
+        -H "Accept: application/vnd.github+json" \
+        "${auth_args[@]}" \
+        "https://api.github.com${path}"
+}
+
+list_versions() {
+    local tool="$1" owner repo
+
+    if ! jq -e --arg tool "$tool" '.[$tool]' "$MANIFEST" >/dev/null; then
+        printf 'Unsupported tool: %s\n' "$tool" >&2
+        exit 1
+    fi
+
+    owner="$(jq -r --arg tool "$tool" '.[$tool].owner' "$MANIFEST")"
+    repo="$(jq -r --arg tool "$tool" '.[$tool].repo' "$MANIFEST")"
+
+    github_api "/repos/$owner/$repo/releases?per_page=100" | jq -r '.[].tag_name'
+}
+
+select_version() {
+    local tool="$1"
+    local versions
+
+    versions="$(list_versions "$tool")"
+
+    if [ -z "$versions" ]; then
+        printf 'No releases found for %s\n' "$tool" >&2
+        exit 1
+    fi
+
+    if command -v fzf >/dev/null 2>&1; then
+        printf '%s\n' "$versions" | fzf --prompt="Select ${tool} version > " --height=20 --reverse
+    else
+        printf '%s\n' "$versions" | sed -n '1,20p' >&2
+        printf 'fzf is not installed, so pass a version explicitly.\n' >&2
+        exit 1
+    fi
+}
+
+update_version() {
+    local tool="$1" version="$2"
+    local tmp_file
+
+    if [ -z "$version" ]; then
+        printf 'No version selected for %s\n' "$tool" >&2
+        exit 1
+    fi
+
+    tmp_file="$(mktemp)"
+    python3 - "$MANIFEST" "$tool" "$version" "$tmp_file" <<'PY'
+import json
+import pathlib
+import sys
+
+manifest_path = pathlib.Path(sys.argv[1])
+tool = sys.argv[2]
+version = sys.argv[3]
+tmp_path = pathlib.Path(sys.argv[4])
+
+data = json.loads(manifest_path.read_text())
+if tool not in data:
+    raise SystemExit(f"Unsupported tool: {tool}")
+
+data[tool]["version"] = version
+tmp_path.write_text(json.dumps(data, indent=2) + "\n")
+PY
+
+    mv "$tmp_file" "$MANIFEST"
+    printf 'Pinned %s to %s\n' "$tool" "$version"
+}
+
+main() {
+    local mode="update" tool version
+
+    ensure_deps
+
+    if [ "${1:-}" = "--list" ]; then
+        mode="list"
+        shift
+    fi
+
+    tool="${1:-}"
+    version="${2:-}"
+
+    if [ -z "$tool" ]; then
+        printf 'Usage: %s [--list] tool [version]\n' "$0" >&2
+        exit 1
+    fi
+
+    case "$mode" in
+        list)
+            list_versions "$tool"
+            ;;
+        update)
+            if [ -z "$version" ]; then
+                version="$(select_version "$tool")"
+            fi
+            update_version "$tool" "$version"
+            ;;
+    esac
+}
+
+main "$@"

Scripts/cpp.sh

@@ -1,6 +1,6 @@
 #!/bin/bash
 
-# Path: scripts/cpp.sh
+# Path: Scripts/cpp.sh
 
 set -e
 

Scripts/go.sh

@@ -1,6 +1,6 @@
 #!/bin/bash
 
-# Path: scripts/go.sh
+# Path: Scripts/go.sh
 
 set -e
 

Scripts/node.sh

@@ -1,6 +1,6 @@
 #!/bin/bash
 
-# Path: scripts/node.sh
+# Path: Scripts/node.sh
 
 set -e
 

Scripts/provision.sh

@@ -1,6 +1,6 @@
 #!/bin/bash
 
-# Path: scripts/provision.sh
+# Path: Scripts/provision.sh
 
 set -e
 

Scripts/python.sh

@@ -1,6 +1,6 @@
 #!/bin/bash
 
-# Path: scripts/python.sh
+# Path: Scripts/python.sh
 set -e
 
 BLUE='\033[1;34m'

Scripts/r.sh

@@ -1,6 +1,6 @@
 #!/bin/bash
 
-# Path: scripts/r.sh
+# Path: Scripts/r.sh
 set -e
 
 BLUE='\033[1;34m'
@@ -12,6 +12,27 @@ NC='\033[0m'
 SCRIPT_DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
 source "$SCRIPT_DIR/lib/distro.sh"
 
+PROG_DIR="$HOME/.programming"
+R_ROOT="$PROG_DIR/r"
+R_BIN_DIR="$R_ROOT/bin"
+R_LIB_DIR="$R_ROOT/library"
+
+mkdir -p "$R_BIN_DIR" "$R_LIB_DIR"
+
+write_r_wrapper() {
+    local target_name="$1"
+    local command_body="$2"
+
+    cat > "$R_BIN_DIR/$target_name" <<EOF
+#!/bin/bash
+set -e
+export R_LIBS_USER="$R_LIB_DIR"
+$command_body "\$@"
+EOF
+
+    chmod +x "$R_BIN_DIR/$target_name"
+}
+
 echo -e "${BLUE}    LOG:${YELLOW} Detecting R installation strategy for $OS...${NC}"
 
 if is_arch_family; then
@@ -30,6 +51,8 @@ if is_arch_family; then
     echo -e "${GREEN}    SUCCESS:${NC} R installed via Pacman."
     
     R_BIN="R"
+    write_r_wrapper "R" 'exec "$(command -v R)"'
+    write_r_wrapper "Rscript" 'exec "$(command -v Rscript)"'
 
 elif is_debian_family; then
 
@@ -77,6 +100,8 @@ elif is_debian_family; then
     fi
     
     R_BIN="rig run"
+    write_r_wrapper "R" 'exec rig run'
+    write_r_wrapper "Rscript" 'exec rig run Rscript'
 
 elif is_fedora_family; then
 
@@ -90,14 +115,18 @@ elif is_fedora_family; then
     fi
 
     R_BIN="R"
+    write_r_wrapper "R" 'exec "$(command -v R)"'
+    write_r_wrapper "Rscript" 'exec "$(command -v Rscript)"'
 
 else
     echo -e "${RED}    ERROR:${NC} Unsupported OS: $OS"
     exit 1
 fi
 
+export R_LIBS_USER="$R_LIB_DIR"
+
 echo -e "${BLUE}    LOG:${YELLOW} Installing 'renv' package in the user R library...${NC}"
 
-$R_BIN -e 'user_lib <- path.expand(Sys.getenv("R_LIBS_USER", unset = "~/R/library")); dir.create(user_lib, recursive = TRUE, showWarnings = FALSE); .libPaths(c(user_lib, .libPaths())); if (!require("renv", quietly=TRUE)) install.packages("renv", lib = user_lib, repos = "https://cloud.r-project.org")'
+$R_BIN -e 'user_lib <- path.expand(Sys.getenv("R_LIBS_USER", unset = "~/.programming/r/library")); dir.create(user_lib, recursive = TRUE, showWarnings = FALSE); .libPaths(c(user_lib, .libPaths())); if (!require("renv", quietly=TRUE)) install.packages("renv", lib = user_lib, repos = "https://cloud.r-project.org")'
 
 echo -e "${GREEN}    SUCCESS:${NC} R setup completed."

Scripts/rust.sh

@@ -1,6 +1,6 @@
 #!/bin/bash
 
-# Path: scripts/rust.sh
+# Path: Scripts/rust.sh
 
 set -e
 
@@ -38,4 +38,4 @@ if command -v cargo &> /dev/null; then
 else
     echo -e "${RED}    ERROR: Cargo not found in PATH. Check CARGO_HOME.${NC}"
     exit 1
-fi
+fi

Scripts/setup.sh

@@ -0,0 +1,68 @@
+#!/bin/bash
+
+set -euo pipefail
+
+SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
+REPO_ROOT="$(dirname "$SCRIPT_DIR")"
+REBOOT_MARKER="$REPO_ROOT/.setup-reboot-required"
+REPO_SECRET_FILE="$REPO_ROOT/Zsh/.zsh_secrets"
+HOME_SECRET_FILE="$HOME/.zsh_secrets"
+
+handle_reboot_marker() {
+    if [ -f "$REBOOT_MARKER" ]; then
+        rm -f "$REBOOT_MARKER"
+        echo "Package layering finished. Reboot, then rerun the same command."
+        exit 0
+    fi
+}
+
+sync_repo_managed_secret_file() {
+    mkdir -p "$(dirname "$REPO_SECRET_FILE")"
+
+    if [ -L "$HOME_SECRET_FILE" ]; then
+        return 0
+    fi
+
+    if [ -f "$HOME_SECRET_FILE" ]; then
+        if [ ! -f "$REPO_SECRET_FILE" ] || [ ! -s "$REPO_SECRET_FILE" ]; then
+            mv "$HOME_SECRET_FILE" "$REPO_SECRET_FILE"
+            return 0
+        fi
+
+        if cmp -s "$HOME_SECRET_FILE" "$REPO_SECRET_FILE"; then
+            rm -f "$HOME_SECRET_FILE"
+            return 0
+        fi
+
+        echo "Conflict: both $HOME_SECRET_FILE and $REPO_SECRET_FILE exist with different contents."
+        echo "Please merge them manually, then rerun the command."
+        exit 1
+    fi
+
+    touch "$REPO_SECRET_FILE"
+}
+
+main() {
+    rm -f "$REBOOT_MARKER"
+
+    bash "$SCRIPT_DIR/base.sh"
+    handle_reboot_marker
+
+    bash "$SCRIPT_DIR/node.sh"
+    bash "$SCRIPT_DIR/go.sh"
+    bash "$SCRIPT_DIR/rust.sh"
+    bash "$SCRIPT_DIR/python.sh"
+    handle_reboot_marker
+
+    bash "$SCRIPT_DIR/r.sh"
+    handle_reboot_marker
+
+    sync_repo_managed_secret_file
+
+    stow --dir="$REPO_ROOT" -D Zsh --target="$HOME" 2>/dev/null || true
+    stow --dir="$REPO_ROOT" Zsh --target="$HOME"
+
+    echo "Full setup completed."
+}
+
+main "$@"

Zsh/.zsh_aliases

@@ -91,4 +91,4 @@ proxy_on() {
 proxy_off() {
     unset ALL_PROXY HTTP_PROXY HTTPS_PROXY
     echo "Proxy OFF (direct)"
-}
+}

Zsh/.zshenv

@@ -4,6 +4,8 @@
 [ -f "$HOME/.zsh_secrets" ] && source "$HOME/.zsh_secrets"
 
 export GOGC=500
+export R_ROOT="$HOME/.programming/r"
+export R_LIBS_USER="$R_ROOT/library"
 
 # CodeGraphContext defaults
 export CGC_RUNTIME_DB_TYPE=kuzudb