diff --git a/cli/bash/commands/basectl/subcommands/setup_common.sh b/cli/bash/commands/basectl/subcommands/setup_common.sh
index 10e2a7d..1c82223 100644
--- a/cli/bash/commands/basectl/subcommands/setup_common.sh
+++ b/cli/bash/commands/basectl/subcommands/setup_common.sh
@@ -437,8 +437,72 @@ setup_base_python_package_check_message() {
     fi
 }
 
+setup_project_setup_pythonpath() {
+    local base_pythonpath old_pythonpath
+
+    base_pythonpath="$BASE_HOME/lib/python:$BASE_HOME/cli/python"
+    old_pythonpath="${PYTHONPATH-}"
+    if [[ -n "$old_pythonpath" ]]; then
+        base_pythonpath="$base_pythonpath:$old_pythonpath"
+    fi
+    printf '%s\n' "$base_pythonpath"
+}
+
+setup_resolve_project_name() {
+    local manifest_arg project python_bin venv_dir
+
+    if [[ -n "${BASE_SETUP_PROJECT_NAME:-}" ]]; then
+        printf '%s\n' "$BASE_SETUP_PROJECT_NAME"
+        return 0
+    fi
+
+    venv_dir="$(setup_venv_dir)"
+    python_bin="$(setup_base_venv_python_bin "$venv_dir")" || fatal_error "Base virtual environment Python was not found at '$venv_dir/bin/python'."
+
+    manifest_arg="${BASE_SETUP_MANIFEST:-}"
+    project="$(
+        env BASE_HOME="$BASE_HOME" PYTHONPATH="$(setup_project_setup_pythonpath)" "$python_bin" -c '
+from pathlib import Path
+import sys
+
+from base_cli.paths import discover_manifest
+from base_setup.manifest import read_manifest
+
+manifest_arg = sys.argv[1]
+start_dir = Path(sys.argv[2])
+if manifest_arg:
+    manifest_path = Path(manifest_arg).expanduser().resolve()
+else:
+    manifest_path = discover_manifest(start_dir)
+
+print(read_manifest(manifest_path).project_name if manifest_path else "base")
+' "$manifest_arg" "$PWD"
+    )" || fatal_error "Unable to resolve Base project name from manifest."
+
+    printf '%s\n' "$project"
+}
+
+setup_validate_dev_project() {
+    local project
+
+    if ! setup_dev_dependencies_enabled; then
+        return 0
+    fi
+
+    if setup_is_dry_run && ! setup_base_python_package_installed "$(setup_pyyaml_package)"; then
+        log_info "[DRY-RUN] Would validate that --dev is only used for the Base project after PyYAML is installed."
+        return 0
+    fi
+
+    project="$(setup_resolve_project_name)"
+    if [[ "$project" != base ]]; then
+        print_error "--dev is only supported for the Base project. Run without --dev for project '$project'."
+        return 1
+    fi
+}
+
 setup_run_project_artifact_setup() {
-    local exit_code project wrapper
+    local exit_code project python_bin venv_dir
     local args=()
 
     if setup_is_dry_run && ! setup_base_python_package_installed "$(setup_pyyaml_package)"; then
@@ -446,20 +510,22 @@ setup_run_project_artifact_setup() {
         return 0
     fi
 
-    project="${BASE_SETUP_PROJECT_NAME:-base}"
-    wrapper="$BASE_HOME/bin/base-wrapper"
-    [[ -x "$wrapper" ]] || fatal_error "Base Python wrapper '$wrapper' is missing or is not executable."
+    venv_dir="$(setup_venv_dir)"
+    python_bin="$(setup_base_venv_python_bin "$venv_dir")" || fatal_error "Base virtual environment Python was not found at '$venv_dir/bin/python'."
+    project="$(setup_resolve_project_name)"
 
     if setup_is_dry_run; then
         args+=(--dry-run)
     fi
     if [[ -n "${BASE_SETUP_MANIFEST:-}" ]]; then
         args+=(--manifest "$BASE_SETUP_MANIFEST")
+    elif [[ "$project" == base ]]; then
+        args+=(--manifest "$BASE_HOME/base_manifest.yaml")
     fi
     args+=("$project")
 
     log_info "Running Python project setup layer."
-    "$wrapper" --project "$project" base_setup "${args[@]}"
+    env BASE_HOME="$BASE_HOME" BASE_PROJECT="$project" PYTHONPATH="$(setup_project_setup_pythonpath)" "$python_bin" -m base_setup "${args[@]}"
     exit_code=$?
 
     exit_if_error "$exit_code" "Python project setup layer failed."
@@ -674,13 +740,14 @@ setup_run_install() {
     setup_install_homebrew
     setup_install_xcode_tools
     setup_install_python
+    setup_create_virtualenv
+    setup_install_pyyaml
+    setup_install_click
+    setup_validate_dev_project || return 1
     if setup_dev_dependencies_enabled; then
         setup_install_bats
         setup_install_gh
     fi
-    setup_create_virtualenv
-    setup_install_pyyaml
-    setup_install_click
     setup_run_project_artifact_setup
 
     if setup_is_dry_run; then
diff --git a/cli/bash/commands/basectl/tests/setup.bats b/cli/bash/commands/basectl/tests/setup.bats
index f42ea0e..344d415 100644
--- a/cli/bash/commands/basectl/tests/setup.bats
+++ b/cli/bash/commands/basectl/tests/setup.bats
@@ -102,9 +102,16 @@ if [[ "${1:-}" == "-m" && "${2:-}" == "venv" && -n "${3:-}" ]]; then
 pyyaml_package="${BASE_SETUP_PYYAML_PACKAGE:-PyYAML}"
 click_package="${BASE_SETUP_CLICK_PACKAGE:-click}"
 if [[ "${1:-}" == "-m" && "${2:-}" == "base_setup" ]]; then
+    shift 2
+    printf '%s\n' "$@" > "${BASE_SETUP_TEST_STATE_DIR:?}/project-setup-args"
+    printf '%s\n' "${BASE_PROJECT:-}" > "${BASE_SETUP_TEST_STATE_DIR:?}/project-setup-project"
     touch "${BASE_SETUP_TEST_STATE_DIR:?}/project-setup-ran"
     exit 0
 fi
+if [[ "${1:-}" == "-c" ]]; then
+    printf 'base\n'
+    exit 0
+fi
 if [[ "${1:-}" == "-m" && "${2:-}" == "pip" && "${3:-}" == "show" && "${4:-}" == "$pyyaml_package" ]]; then
     [[ -f "${BASE_SETUP_TEST_STATE_DIR:?}/pyyaml-installed" ]]
     exit $?
@@ -130,9 +137,16 @@ VENVEOF
     exit 0
 fi
 if [[ "${1:-}" == "-m" && "${2:-}" == "base_setup" ]]; then
+    shift 2
+    printf '%s\n' "$@" > "${BASE_SETUP_TEST_STATE_DIR:?}/project-setup-args"
+    printf '%s\n' "${BASE_PROJECT:-}" > "${BASE_SETUP_TEST_STATE_DIR:?}/project-setup-project"
     touch "${BASE_SETUP_TEST_STATE_DIR:?}/project-setup-ran"
     exit 0
 fi
+if [[ "${1:-}" == "-c" ]]; then
+    printf 'base\n'
+    exit 0
+fi
 printf 'unexpected python3 args: %s\n' "$*" >&2
 exit 1
 PYEOF
@@ -218,9 +232,16 @@ if [[ "${1:-}" == "-m" && "${2:-}" == "venv" && -n "${3:-}" ]]; then
 pyyaml_package="${BASE_SETUP_PYYAML_PACKAGE:-PyYAML}"
 click_package="${BASE_SETUP_CLICK_PACKAGE:-click}"
 if [[ "${1:-}" == "-m" && "${2:-}" == "base_setup" ]]; then
+    shift 2
+    printf '%s\n' "$@" > "${BASE_SETUP_TEST_STATE_DIR:?}/project-setup-args"
+    printf '%s\n' "${BASE_PROJECT:-}" > "${BASE_SETUP_TEST_STATE_DIR:?}/project-setup-project"
     touch "${BASE_SETUP_TEST_STATE_DIR:?}/project-setup-ran"
     exit 0
 fi
+if [[ "${1:-}" == "-c" ]]; then
+    printf 'base\n'
+    exit 0
+fi
 if [[ "${1:-}" == "-m" && "${2:-}" == "pip" && "${3:-}" == "show" && "${4:-}" == "$pyyaml_package" ]]; then
     [[ -f "${BASE_SETUP_TEST_STATE_DIR:?}/pyyaml-installed" ]]
     exit $?
@@ -246,9 +267,16 @@ VENVEOF
     exit 0
 fi
 if [[ "${1:-}" == "-m" && "${2:-}" == "base_setup" ]]; then
+    shift 2
+    printf '%s\n' "$@" > "${BASE_SETUP_TEST_STATE_DIR:?}/project-setup-args"
+    printf '%s\n' "${BASE_PROJECT:-}" > "${BASE_SETUP_TEST_STATE_DIR:?}/project-setup-project"
     touch "${BASE_SETUP_TEST_STATE_DIR:?}/project-setup-ran"
     exit 0
 fi
+if [[ "${1:-}" == "-c" ]]; then
+    printf 'base\n'
+    exit 0
+fi
 printf 'unexpected python3 args: %s\n' "$*" >&2
 exit 1
 PYEOF
@@ -360,6 +388,15 @@ if [[ "${1:-}" == "-m" && "${2:-}" == "base_setup" ]]; then
     touch "$BASE_SETUP_TEST_STATE_DIR/project-setup-ran"
     exit "$(cat "$BASE_SETUP_TEST_STATE_DIR/project-setup-exit-code")"
 fi
+if [[ "${1:-}" == "-c" ]]; then
+    manifest_path="${3:-}"
+    if [[ -n "$manifest_path" && -f "$manifest_path" ]]; then
+        awk '/^[[:space:]]*name:/ { print $2; exit }' "$manifest_path"
+    else
+        printf 'base\n'
+    fi
+    exit 0
+fi
 if [[ "${1:-}" == "-m" && "${2:-}" == "pip" && "${3:-}" == "show" && "${4:-}" == "$pyyaml_package" ]]; then
     [[ -f "${BASE_SETUP_TEST_STATE_DIR:?}/pyyaml-installed" ]]
     exit $?
@@ -503,7 +540,7 @@ EOF
     [ -f "$venv_dir/pyvenv.cfg" ]
 }
 
-@test "basectl setup forwards project setup arguments through base-wrapper" {
+@test "basectl setup forwards explicit project setup arguments through the Base venv" {
     local base_venv_dir="$TEST_HOME/.base.d/base/.venv"
     local demo_venv_dir="$TEST_HOME/.base.d/demo/.venv"
     local manifest_path="$TEST_TMPDIR/demo_manifest.yaml"
@@ -515,8 +552,7 @@ EOF
     touch "$TEST_STATE_DIR/python-installed"
     touch "$TEST_STATE_DIR/pyyaml-installed"
     touch "$TEST_STATE_DIR/click-installed"
-    create_base_venv_stub "$base_venv_dir"
-    create_project_setup_venv_stub "$demo_venv_dir"
+    create_project_setup_venv_stub "$base_venv_dir"
     printf 'project:\n  name: demo\nartifacts: []\n' > "$manifest_path"
 
     run_base_command setup --dry-run --manifest "$manifest_path" demo
@@ -526,6 +562,56 @@ EOF
     [ -f "$TEST_STATE_DIR/project-setup-ran" ]
     [ "$(cat "$TEST_STATE_DIR/project-setup-project")" = "demo" ]
     [ "$(cat "$TEST_STATE_DIR/project-setup-args")" = "$(printf '%s\n' --dry-run --manifest "$manifest_path" demo)" ]
+    [ ! -e "$demo_venv_dir/bin/python" ]
+}
+
+@test "basectl setup infers omitted project argument from the manifest" {
+    local base_venv_dir="$TEST_HOME/.base.d/base/.venv"
+    local demo_venv_dir="$TEST_HOME/.base.d/demo/.venv"
+    local manifest_path="$TEST_TMPDIR/demo_manifest.yaml"
+
+    create_brew_stub
+    create_xcode_stubs
+    touch "$TEST_STATE_DIR/xcode-installed"
+    mkdir -p "$TEST_TMPDIR/CommandLineTools"
+    touch "$TEST_STATE_DIR/python-installed"
+    touch "$TEST_STATE_DIR/pyyaml-installed"
+    touch "$TEST_STATE_DIR/click-installed"
+    create_project_setup_venv_stub "$base_venv_dir"
+    printf 'project:\n  name: demo\nartifacts: []\n' > "$manifest_path"
+
+    run_base_command setup --dry-run --manifest "$manifest_path"
+
+    [ "$status" -eq 0 ]
+    [ -f "$TEST_STATE_DIR/project-setup-ran" ]
+    [ "$(cat "$TEST_STATE_DIR/project-setup-project")" = "demo" ]
+    [ "$(cat "$TEST_STATE_DIR/project-setup-args")" = "$(printf '%s\n' --dry-run --manifest "$manifest_path" demo)" ]
+    [ ! -e "$demo_venv_dir/bin/python" ]
+}
+
+@test "basectl setup --dev fails for non-Base projects before installing developer dependencies" {
+    local base_venv_dir="$TEST_HOME/.base.d/base/.venv"
+    local manifest_path="$TEST_TMPDIR/demo_manifest.yaml"
+
+    create_brew_stub
+    create_xcode_stubs
+    touch "$TEST_STATE_DIR/xcode-installed"
+    mkdir -p "$TEST_TMPDIR/CommandLineTools"
+    touch "$TEST_STATE_DIR/python-installed"
+    touch "$TEST_STATE_DIR/pyyaml-installed"
+    touch "$TEST_STATE_DIR/click-installed"
+    create_project_setup_venv_stub "$base_venv_dir"
+    printf 'project:\n  name: demo\nartifacts: []\n' > "$manifest_path"
+
+    run_base_command setup --dev --manifest "$manifest_path"
+
+    [ "$status" -eq 1 ]
+    [[ "$output" == *"--dev is only supported for the Base project. Run without --dev for project 'demo'."* ]]
+    [[ "$output" != *"FATAL"* ]]
+    [[ "$output" != *"Encountered a fatal error"* ]]
+    [ ! -f "$TEST_STATE_DIR/bats-install-ran" ]
+    [ ! -f "$TEST_STATE_DIR/gh-install-ran" ]
+    [ ! -f "$TEST_STATE_DIR/project-setup-ran" ]
 }
 
 @test "basectl setup propagates Python project setup failure" {
@@ -549,6 +635,7 @@ EOF
 
 @test "basectl setup --dev installs developer dependencies" {
     local installer
+    local expected_args
 
     create_xcode_stubs
     installer="$(create_homebrew_installer_stub)"
@@ -563,6 +650,8 @@ EOF
     [[ "$output" == *"Installing GitHub CLI formula 'gh' via Homebrew."* ]]
     [ -f "$TEST_STATE_DIR/bats-install-ran" ]
     [ -f "$TEST_STATE_DIR/gh-install-ran" ]
+    expected_args="$(printf '%s\n' --manifest "$BASE_REPO_ROOT/base_manifest.yaml" base)"
+    [ "$(cat "$TEST_STATE_DIR/project-setup-args")" = "$expected_args" ]
 }
 
 @test "basectl setup backs up an existing non-venv path before creating the Base virtual environment" {