diff --git a/scripts/e2e/daemon-worktree-setup-e2e.sh b/scripts/e2e/daemon-worktree-setup-e2e.sh
new file mode 100755
index 0000000..36fe562
--- /dev/null
+++ b/scripts/e2e/daemon-worktree-setup-e2e.sh
@@ -0,0 +1,115 @@
+#!/usr/bin/env bash
+# End-to-end harness for issue #78: headless daemon worktree creation
+# runs setup scripts + worktree includes (desktop parity).
+#
+# Stands up a clean containerized host (no desktop, no dev environment),
+# mounts the built `codemux-remote` binary, seeds a git repo with a
+# committed `.codemux/config.json` setup script and a gitignored `.env`,
+# starts `codemux-remote serve`, then drives the REAL authed HTTP tool
+# surface (`tools/call worktree_create`) exactly like the MCP bridge
+# does — and asserts on the container's filesystem that:
+#   1. the worktree was created at the canonical path,
+#   2. the setup script ran with CODEMUX_BRANCH/CODEMUX_PORT injected,
+#   3. the gitignored .env was copied from the main checkout.
+#
+# Requires: docker, python3, and a debug build of codemux-remote
+# (`cargo build --manifest-path src-tauri/Cargo.toml --bin codemux-remote`).
+# Run from the repo root:  bash scripts/e2e/daemon-worktree-setup-e2e.sh
+# Override the binary under test with CMX_WT_E2E_BIN=/path/to/codemux-remote.
+set -euo pipefail
+
+REPO_ROOT="$(cd "$(dirname "${BASH_SOURCE[0]}")/../.." && pwd)"
+BIN="${CMX_WT_E2E_BIN:-$REPO_ROOT/src-tauri/target/debug/codemux-remote}"
+IMAGE="${CMX_WT_E2E_IMAGE:-archlinux:latest}"
+CONTAINER="codemux-worktree-setup-e2e"
+
+log() { printf '\n\033[1;36m[e2e]\033[0m %s\n' "$*"; }
+err() { printf '\n\033[1;31m[e2e:ERROR]\033[0m %s\n' "$*" >&2; }
+
+cleanup() {
+  docker rm -f "$CONTAINER" >/dev/null 2>&1 || true
+}
+trap cleanup EXIT
+
+command -v docker >/dev/null || { err "docker not found"; exit 1; }
+[ -x "$BIN" ] || { err "codemux-remote not built at $BIN"; exit 1; }
+
+log "starting clean host container ($IMAGE)"
+docker rm -f "$CONTAINER" >/dev/null 2>&1 || true
+docker run -d --name "$CONTAINER" \
+  -v "$BIN":/usr/local/bin/codemux-remote:ro \
+  "$IMAGE" sleep infinity >/dev/null
+
+log "installing git + runtime libs in the container"
+# The codemux-remote bin target shares the desktop crate, so the debug
+# binary dynamically links gtk/webkit even though serve never uses them.
+docker exec "$CONTAINER" pacman -Sy --noconfirm git gtk3 webkit2gtk-4.1 >/dev/null 2>&1
+
+log "seeding repo with setup config + gitignored .env"
+docker exec -i "$CONTAINER" bash -eu -o pipefail <<'SEED'
+git config --global user.email t@e.com
+git config --global user.name T
+git config --global init.defaultBranch main
+mkdir -p /root/repo/.codemux
+cd /root/repo
+git init -q
+# Single-quoted heredoc below keeps $CODEMUX_* literal for the daemon.
+cat > .codemux/config.json <<'CFG'
+{ "setup": ["printf '%s\n%s\n' \"$CODEMUX_BRANCH\" \"$CODEMUX_PORT\" > setup-ran.txt"] }
+CFG
+printf '.env\n' > .gitignore
+printf 'SECRET=docker-host\n' > .env
+printf 'x\n' > f.txt
+git add .
+git commit -qm init
+SEED
+
+log "starting codemux-remote serve"
+docker exec -d "$CONTAINER" bash -c \
+  'mkdir -p /root/state && codemux-remote serve --state-dir /root/state > /root/state/serve.log 2>&1'
+
+log "waiting for manifest"
+for i in $(seq 1 50); do
+  if docker exec "$CONTAINER" test -f /root/state/manifest.json; then break; fi
+  sleep 0.2
+done
+docker exec "$CONTAINER" test -f /root/state/manifest.json || {
+  err "daemon never wrote manifest"; docker exec "$CONTAINER" cat /root/state/serve.log || true; exit 1;
+}
+
+MANIFEST="$(docker exec "$CONTAINER" cat /root/state/manifest.json)"
+ENDPOINT="$(printf '%s' "$MANIFEST" | python3 -c 'import sys,json;print(json.load(sys.stdin)["endpoint"])')"
+SECRET="$(printf '%s' "$MANIFEST" | python3 -c 'import sys,json;print(json.load(sys.stdin)["secret"])')"
+log "daemon live at $ENDPOINT"
+
+log "calling tools/call worktree_create over authed HTTP"
+RESPONSE="$(docker exec "$CONTAINER" curl -sf -X POST "$ENDPOINT/tools/call" \
+  -H "Authorization: Bearer $SECRET" \
+  -H 'Content-Type: application/json' \
+  -d '{"name":"worktree_create","arguments":{"repo_path":"/root/repo","branch":"feature/provision","base":"main"}}')"
+printf '%s\n' "$RESPONSE" | python3 -m json.tool
+
+WS_PATH="$(printf '%s' "$RESPONSE" | python3 -c 'import sys,json;print(json.load(sys.stdin)["data"]["workspace"]["path"])')"
+RUNNING="$(printf '%s' "$RESPONSE" | python3 -c 'import sys,json;print(json.load(sys.stdin)["data"]["setup"]["setup_running"])')"
+PORT="$(printf '%s' "$RESPONSE" | python3 -c 'import sys,json;print(json.load(sys.stdin)["data"]["setup"]["port"])')"
+[ "$RUNNING" = "True" ] || { err "setup.setup_running should be true"; exit 1; }
+
+log "worktree at $WS_PATH — polling for setup marker"
+MARKER="$WS_PATH/setup-ran.txt"
+for i in $(seq 1 100); do
+  if docker exec "$CONTAINER" test -f "$MARKER"; then break; fi
+  sleep 0.2
+done
+docker exec "$CONTAINER" test -f "$MARKER" || {
+  err "setup script never ran"; docker exec "$CONTAINER" cat /root/state/serve.log || true; exit 1;
+}
+
+GOT_BRANCH="$(docker exec "$CONTAINER" sed -n 1p "$MARKER")"
+GOT_PORT="$(docker exec "$CONTAINER" sed -n 2p "$MARKER")"
+GOT_ENV="$(docker exec "$CONTAINER" cat "$WS_PATH/.env")"
+
+[ "$GOT_BRANCH" = "feature/provision" ] || { err "CODEMUX_BRANCH wrong: $GOT_BRANCH"; exit 1; }
+[ "$GOT_PORT" = "$PORT" ] || { err "CODEMUX_PORT mismatch: $GOT_PORT vs $PORT"; exit 1; }
+[ "$GOT_ENV" = "SECRET=docker-host" ] || { err ".env not copied: $GOT_ENV"; exit 1; }
+
+log "PASS — daemon-created worktree was provisioned (setup script ran with branch=$GOT_BRANCH port=$GOT_PORT, .env copied)"