diff --git a/scripts/conductor-scripts.test.mjs b/scripts/conductor-scripts.test.mjs
index ba0ac88e..3e83887b 100644
--- a/scripts/conductor-scripts.test.mjs
+++ b/scripts/conductor-scripts.test.mjs
@@ -17,49 +17,26 @@ describe('Conductor workspace scripts', () => {
     assert.equal(manifest.runScriptMode, 'nonconcurrent');
   });
 
-  it('orchestrates setup through focused step scripts', async () => {
+  it('sets up exact uv, local files, Python packages, JS packages, and the built CLI', async () => {
     const setupScript = await readText('scripts/conductor-setup.sh');
 
-    assert.match(setupScript, /sh scripts\/conductor\/link-agent-overlays\.sh/);
-    assert.match(setupScript, /sh scripts\/conductor\/link-root-env-file\.sh/);
-    assert.match(setupScript, /source scripts\/conductor\/activate-workspace-uv\.sh/);
-    assert.match(setupScript, /sh scripts\/conductor\/install-python-dependencies\.sh/);
-    assert.match(setupScript, /sh scripts\/conductor\/install-js-dependencies\.sh/);
-    assert.match(setupScript, /sh scripts\/conductor\/rebuild-native-dependencies\.sh/);
-    assert.match(setupScript, /sh scripts\/conductor\/build-workspace\.sh/);
-    assert.match(setupScript, /sh scripts\/conductor\/run-setup-doctor\.sh/);
-    assert.doesNotMatch(setupScript, /read_required_uv_version\(\)/);
-    assert.doesNotMatch(setupScript, /uv sync --all-packages --all-groups/);
-    assert.doesNotMatch(setupScript, /pnpm install --frozen-lockfile --prefer-offline/);
-    assert.doesNotMatch(setupScript, /packages\/cli\/dist\/bin\.js dev doctor setup --no-input/);
-  });
-
-  it('keeps concrete setup commands in step scripts', async () => {
-    const resolveUvScript = await readText('scripts/conductor/resolve-uv.sh');
-    const activateUvScript = await readText('scripts/conductor/activate-workspace-uv.sh');
-    const pythonScript = await readText('scripts/conductor/install-python-dependencies.sh');
-    const jsScript = await readText('scripts/conductor/install-js-dependencies.sh');
-    const nativeScript = await readText('scripts/conductor/rebuild-native-dependencies.sh');
-    const buildScript = await readText('scripts/conductor/build-workspace.sh');
-    const doctorScript = await readText('scripts/conductor/run-setup-doctor.sh');
-
-    assert.match(resolveUvScript, /read_required_uv_version\(\)/);
-    assert.match(resolveUvScript, /\.context\/bin\/uv-\$required_version/);
-    assert.match(activateUvScript, /bash scripts\/conductor\/resolve-uv\.sh pyproject\.toml/);
-    assert.match(activateUvScript, /export PATH="\$\(dirname "\$KTX_UV_BIN"\):\$PATH"/);
-    assert.match(pythonScript, /uv sync --all-packages --all-groups/);
-    assert.match(jsScript, /pnpm install --frozen-lockfile --prefer-offline/);
-    assert.match(nativeScript, /pnpm run native:rebuild/);
-    assert.match(buildScript, /pnpm run build/);
-    assert.match(doctorScript, /packages\/cli\/dist\/bin\.js dev doctor setup --no-input/);
+    assert.match(setupScript, /read_required_uv_version\(\)/);
+    assert.match(setupScript, /\.context\/bin\/uv-\$required_version/);
+    assert.match(setupScript, /link_agent_overlays/);
+    assert.match(setupScript, /CONDUCTOR_ROOT_PATH/);
+    assert.match(setupScript, /uv sync --all-packages --all-groups/);
+    assert.match(setupScript, /pnpm install --frozen-lockfile --prefer-offline/);
+    assert.match(setupScript, /pnpm run native:rebuild/);
+    assert.match(setupScript, /pnpm run build/);
+    assert.match(setupScript, /packages\/cli\/dist\/bin\.js dev doctor setup --no-input/);
+    assert.doesNotMatch(setupScript, /scripts\/conductor\//);
   });
 
   it('links private agent overlays when KAELIO_SKILLS_ROOT is set', async () => {
-    const workspaceScript = await readText('scripts/conductor/link-agent-overlays.sh');
+    const workspaceScript = await readText('scripts/conductor-setup.sh');
 
     assert.match(workspaceScript, /KAELIO_SKILLS_ROOT/);
-    assert.match(workspaceScript, /agents_source="\$\{KAELIO_SKILLS_ROOT\}\/\.agents"/);
-    assert.match(workspaceScript, /ln -s "\$\{agents_source\}" \.agents/);
+    assert.match(workspaceScript, /ln -s "\$\{KAELIO_SKILLS_ROOT\}\/\.agents" \.agents/);
   });
 
   it('runs the KTX daemon on the documented fixed local port', async () => {
diff --git a/scripts/conductor-setup.sh b/scripts/conductor-setup.sh
index 8837a9ab..ee0271c4 100755
--- a/scripts/conductor-setup.sh
+++ b/scripts/conductor-setup.sh
@@ -1,20 +1,129 @@
 #!/bin/bash
 # conductor-setup.sh - Runs once when Conductor creates a KTX workspace.
 #
-# Orchestrates workspace setup. Step implementation lives in scripts/conductor/.
+# Prepares the standalone pnpm + uv workspace and builds the local CLI.
 
 set -e
 set -o pipefail
 
+read_required_uv_version() {
+  local project_file="$1"
+
+  if [ ! -f "$project_file" ]; then
+    return 1
+  fi
+
+  sed -nE 's/^[[:space:]]*required-version[[:space:]]*=[[:space:]]*"([^"]+)".*/\1/p' "$project_file" | head -n 1
+}
+
+uv_version() {
+  local uv_bin="$1"
+
+  "$uv_bin" --version 2>/dev/null | awk '{print $2}'
+}
+
+install_workspace_uv() {
+  local required_version="$1"
+  local install_dir="$PWD/.context/bin/uv-$required_version"
+
+  mkdir -p "$install_dir"
+
+  if [ ! -x "$install_dir/uv" ] || [ "$(uv_version "$install_dir/uv")" != "$required_version" ]; then
+    echo "Installing workspace-local uv $required_version..." >&2
+    curl -LsSf "https://astral.sh/uv/$required_version/install.sh" |
+      env UV_INSTALL_DIR="$install_dir" UV_NO_MODIFY_PATH=1 sh >&2
+  fi
+
+  printf '%s\n' "$install_dir/uv"
+}
+
+resolve_uv_for_project() {
+  local project_file="$1"
+  local required_version
+  local system_uv
+  local system_version
+  local workspace_uv
+
+  required_version="$(read_required_uv_version "$project_file" || true)"
+  required_version="${required_version#==}"
+
+  if [ -z "$required_version" ]; then
+    command -v uv
+    return
+  fi
+
+  if ! [[ "$required_version" =~ ^[0-9]+[.][0-9]+[.][0-9]+$ ]]; then
+    echo "WARNING: Unsupported uv required-version '$required_version'; using uv from PATH." >&2
+    command -v uv
+    return
+  fi
+
+  if command -v uv >/dev/null 2>&1; then
+    system_uv="$(command -v uv)"
+    system_version="$(uv_version "$system_uv")"
+
+    if [ "$system_version" = "$required_version" ]; then
+      printf '%s\n' "$system_uv"
+      return
+    fi
+
+    echo "Found uv $system_version at $system_uv; $project_file requires uv $required_version." >&2
+  else
+    echo "uv is not installed on PATH; $project_file requires uv $required_version." >&2
+  fi
+
+  workspace_uv="$(install_workspace_uv "$required_version")"
+
+  if [ "$(uv_version "$workspace_uv")" != "$required_version" ]; then
+    echo "ERROR: Expected uv $required_version at $workspace_uv, got $("$workspace_uv" --version 2>&1 || true)." >&2
+    return 1
+  fi
+
+  printf '%s\n' "$workspace_uv"
+}
+
+link_agent_overlays() {
+  if [ -z "${KAELIO_SKILLS_ROOT:-}" ] || [ ! -d "${KAELIO_SKILLS_ROOT}/.agents" ]; then
+    return 0
+  fi
+
+  if [ -L .agents ]; then
+    return 0
+  fi
+
+  if [ -e .agents ]; then
+    echo "Skipping .agents symlink because .agents already exists and is not a symlink." >&2
+    return 0
+  fi
+
+  ln -s "${KAELIO_SKILLS_ROOT}/.agents" .agents
+}
+
 echo "=== Conductor KTX workspace setup ==="
 
-sh scripts/conductor/link-agent-overlays.sh
-sh scripts/conductor/link-root-env-file.sh
-source scripts/conductor/activate-workspace-uv.sh
-sh scripts/conductor/install-python-dependencies.sh
-sh scripts/conductor/install-js-dependencies.sh
-sh scripts/conductor/rebuild-native-dependencies.sh
-sh scripts/conductor/build-workspace.sh
-sh scripts/conductor/run-setup-doctor.sh
+link_agent_overlays
+
+if [ -n "${CONDUCTOR_ROOT_PATH:-}" ] && [ -f "$CONDUCTOR_ROOT_PATH/.env" ]; then
+  ln -sf "$CONDUCTOR_ROOT_PATH/.env" .env
+  echo "Linked .env"
+fi
+
+KTX_UV_BIN="$(resolve_uv_for_project "pyproject.toml")"
+export PATH="$(dirname "$KTX_UV_BIN"):$PATH"
+
+echo "Installing KTX Python dependencies..."
+uv sync --all-packages --all-groups
+
+echo "Installing KTX JS dependencies..."
+pnpm install --frozen-lockfile --prefer-offline
+
+echo "Rebuilding native JS dependencies..."
+pnpm run native:rebuild
+
+echo "Building KTX packages..."
+pnpm run build
+
+echo "Running KTX setup doctor..."
+node packages/cli/dist/bin.js dev doctor setup --no-input
 
 echo "=== Setup complete ==="
diff --git a/scripts/conductor/activate-workspace-uv.sh b/scripts/conductor/activate-workspace-uv.sh
deleted file mode 100755
index 306e0eb7..00000000
--- a/scripts/conductor/activate-workspace-uv.sh
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/bin/bash
-set -e
-set -o pipefail
-
-KTX_UV_BIN="$(bash scripts/conductor/resolve-uv.sh pyproject.toml)"
-export PATH="$(dirname "$KTX_UV_BIN"):$PATH"
diff --git a/scripts/conductor/build-workspace.sh b/scripts/conductor/build-workspace.sh
deleted file mode 100755
index 06ce97db..00000000
--- a/scripts/conductor/build-workspace.sh
+++ /dev/null
@@ -1,5 +0,0 @@
-#!/bin/sh
-set -eu
-
-echo "Building KTX packages..."
-pnpm run build
diff --git a/scripts/conductor/install-js-dependencies.sh b/scripts/conductor/install-js-dependencies.sh
deleted file mode 100755
index 0cee55f1..00000000
--- a/scripts/conductor/install-js-dependencies.sh
+++ /dev/null
@@ -1,5 +0,0 @@
-#!/bin/sh
-set -eu
-
-echo "Installing KTX JS dependencies..."
-pnpm install --frozen-lockfile --prefer-offline
diff --git a/scripts/conductor/install-python-dependencies.sh b/scripts/conductor/install-python-dependencies.sh
deleted file mode 100755
index aa297dac..00000000
--- a/scripts/conductor/install-python-dependencies.sh
+++ /dev/null
@@ -1,5 +0,0 @@
-#!/bin/sh
-set -eu
-
-echo "Installing KTX Python dependencies..."
-uv sync --all-packages --all-groups
diff --git a/scripts/conductor/link-agent-overlays.sh b/scripts/conductor/link-agent-overlays.sh
deleted file mode 100755
index 8e84145f..00000000
--- a/scripts/conductor/link-agent-overlays.sh
+++ /dev/null
@@ -1,23 +0,0 @@
-#!/bin/sh
-set -eu
-
-if [ -z "${KAELIO_SKILLS_ROOT:-}" ]; then
-  exit 0
-fi
-
-agents_source="${KAELIO_SKILLS_ROOT}/.agents"
-
-if [ ! -d "${agents_source}" ]; then
-  exit 0
-fi
-
-if [ -L .agents ]; then
-  exit 0
-fi
-
-if [ -e .agents ]; then
-  echo "Skipping .agents symlink because .agents already exists and is not a symlink." >&2
-  exit 0
-fi
-
-ln -s "${agents_source}" .agents
diff --git a/scripts/conductor/link-root-env-file.sh b/scripts/conductor/link-root-env-file.sh
deleted file mode 100755
index 27f6f2dc..00000000
--- a/scripts/conductor/link-root-env-file.sh
+++ /dev/null
@@ -1,7 +0,0 @@
-#!/bin/sh
-set -eu
-
-if [ -n "${CONDUCTOR_ROOT_PATH:-}" ] && [ -f "$CONDUCTOR_ROOT_PATH/.env" ]; then
-  ln -sf "$CONDUCTOR_ROOT_PATH/.env" .env
-  echo "Linked .env"
-fi
diff --git a/scripts/conductor/rebuild-native-dependencies.sh b/scripts/conductor/rebuild-native-dependencies.sh
deleted file mode 100755
index 7a5651ef..00000000
--- a/scripts/conductor/rebuild-native-dependencies.sh
+++ /dev/null
@@ -1,5 +0,0 @@
-#!/bin/sh
-set -eu
-
-echo "Rebuilding native JS dependencies..."
-pnpm run native:rebuild
diff --git a/scripts/conductor/resolve-uv.sh b/scripts/conductor/resolve-uv.sh
deleted file mode 100755
index 9bb70815..00000000
--- a/scripts/conductor/resolve-uv.sh
+++ /dev/null
@@ -1,81 +0,0 @@
-#!/bin/bash
-set -e
-set -o pipefail
-
-read_required_uv_version() {
-  local project_file="$1"
-
-  if [ ! -f "$project_file" ]; then
-    return 1
-  fi
-
-  sed -nE 's/^[[:space:]]*required-version[[:space:]]*=[[:space:]]*"([^"]+)".*/\1/p' "$project_file" | head -n 1
-}
-
-uv_version() {
-  local uv_bin="$1"
-
-  "$uv_bin" --version 2>/dev/null | awk '{print $2}'
-}
-
-install_workspace_uv() {
-  local required_version="$1"
-  local install_dir="$PWD/.context/bin/uv-$required_version"
-
-  mkdir -p "$install_dir"
-
-  if [ ! -x "$install_dir/uv" ] || [ "$(uv_version "$install_dir/uv")" != "$required_version" ]; then
-    echo "Installing workspace-local uv $required_version..." >&2
-    curl -LsSf "https://astral.sh/uv/$required_version/install.sh" |
-      env UV_INSTALL_DIR="$install_dir" UV_NO_MODIFY_PATH=1 sh >&2
-  fi
-
-  printf '%s\n' "$install_dir/uv"
-}
-
-resolve_uv_for_project() {
-  local project_file="$1"
-  local required_version
-  local system_uv
-  local system_version
-  local workspace_uv
-
-  required_version="$(read_required_uv_version "$project_file" || true)"
-  required_version="${required_version#==}"
-
-  if [ -z "$required_version" ]; then
-    command -v uv
-    return
-  fi
-
-  if ! [[ "$required_version" =~ ^[0-9]+[.][0-9]+[.][0-9]+$ ]]; then
-    echo "WARNING: Unsupported uv required-version '$required_version'; using uv from PATH." >&2
-    command -v uv
-    return
-  fi
-
-  if command -v uv >/dev/null 2>&1; then
-    system_uv="$(command -v uv)"
-    system_version="$(uv_version "$system_uv")"
-
-    if [ "$system_version" = "$required_version" ]; then
-      printf '%s\n' "$system_uv"
-      return
-    fi
-
-    echo "Found uv $system_version at $system_uv; $project_file requires uv $required_version." >&2
-  else
-    echo "uv is not installed on PATH; $project_file requires uv $required_version." >&2
-  fi
-
-  workspace_uv="$(install_workspace_uv "$required_version")"
-
-  if [ "$(uv_version "$workspace_uv")" != "$required_version" ]; then
-    echo "ERROR: Expected uv $required_version at $workspace_uv, got $("$workspace_uv" --version 2>&1 || true)." >&2
-    return 1
-  fi
-
-  printf '%s\n' "$workspace_uv"
-}
-
-resolve_uv_for_project "${1:-pyproject.toml}"
diff --git a/scripts/conductor/run-setup-doctor.sh b/scripts/conductor/run-setup-doctor.sh
deleted file mode 100755
index 285aab00..00000000
--- a/scripts/conductor/run-setup-doctor.sh
+++ /dev/null
@@ -1,5 +0,0 @@
-#!/bin/sh
-set -eu
-
-echo "Running KTX setup doctor..."
-node packages/cli/dist/bin.js dev doctor setup --no-input