start-at-login scrambles the vm files

### Description

When using the `start-at-login --enabled=true` command and restarting the host machine, the files on the vm become all scrambled. Some random files are added, and some important ones are now missing...

**EDIT** : it seems that the vm's workdir content gets replaced by the host's `.lima/` content.

I don't this this should be the expected behaviour, or at least something in the documentation should mention it.

Here are the original files :

Here are the files after the start on login restart :

**Informations**

- Host : macOS 15.6.1 (latest)
- lima version : 1.2.1 (latest)
- VM type : vz

effective lima config

```
# BASED ON https://github.com/lima-vm/lima/blob/v1.2.1/templates/docker-rootful.yaml
# A template to use Docker (rootful) instead of containerd & nerdctl

minimumLimaVersion: 1.1.0

# containerd is managed by Docker, not by Lima, so the values are set to false here.
containerd:
system: false
user: false

mounts:
- location: "."
mountPoint: /gitlab-runner
writable: true

- location: "./runner/cache"
mountPoint: /tmp/gitlab_runner_cache
writable: true

provision:
- mode: system
# This script defines the host.docker.internal hostname when hostResolver is disabled.
# It is also needed for lima 0.8.2 and earlier, which does not support hostResolver.hosts.
# Names defined in /etc/hosts inside the VM are not resolved inside containers when
# using the hostResolver; use hostResolver.hosts instead (requires lima 0.8.3 or later).
script: |
#!/bin/sh
sed -i 's/host.lima.internal.*/host.lima.internal host.docker.internal/' /etc/hosts

- mode: system
script: |
#!/bin/bash
set -eux -o pipefail
command -v docker >/dev/null 2>&1 && exit 0
if [ ! -e /etc/systemd/system/docker.socket.d/override.conf ]; then
mkdir -p /etc/systemd/system/docker.socket.d
# Alternatively we could just add the user to the "docker" group, but that requires restarting the user session
cat <<-EOF >/etc/systemd/system/docker.socket.d/override.conf
[Socket]
SocketUser={{.User}}
EOF
fi
export DEBIAN_FRONTEND=noninteractive
curl -fsSL https://get.docker.com | sh

probes:
- script: |
#!/bin/bash
set -eux -o pipefail
if ! timeout 30s bash -c "until command -v docker >/dev/null 2>&1; do sleep 3; done"; then
echo >&2 "docker is not installed yet"
exit 1
fi
if ! timeout 30s bash -c "until pgrep dockerd; do sleep 3; done"; then
echo >&2 "dockerd is not running"
exit 1
fi
hint: See "/var/log/cloud-init-output.log" in the guest

hostResolver:
# hostResolver.hosts requires lima 0.8.3 or later. Names defined here will also
# resolve inside containers, and not just inside the VM itself.
hosts:
host.docker.internal: host.lima.internal

portForwards:
- guestSocket: "/var/run/docker.sock"
hostSocket: "{{.Dir}}/sock/docker.sock"

- guestPort: 9005
hostPort: 9005

images:
# Try to use release-yyyyMMdd image if available. Note that release-yyyyMMdd will be removed after several months.

- location: "https://cloud-images.ubuntu.com/releases/noble/release-20250704/ubuntu-24.04-server-cloudimg-amd64.img"
arch: "x86_64"
digest: "sha256:f1652d29d497fb7c623433705c9fca6525d1311b11294a0f495eed55c7639d1f"
- location: "https://cloud-images.ubuntu.com/releases/noble/release-20250704/ubuntu-24.04-server-cloudimg-arm64.img"
arch: "aarch64"
digest: "sha256:bbecbb88100ee65497927ed0da247ba15af576a8855004182cf3c87265e25d35"
- location: "https://cloud-images.ubuntu.com/releases/noble/release-20250704/ubuntu-24.04-server-cloudimg-riscv64.img"
arch: "riscv64"
digest: "sha256:3694a05d426568b8a8d7c8ac57cf55d5b1b1fc03ece48835bdd53a51874a063c"
- location: "https://cloud-images.ubuntu.com/releases/noble/release-20250704/ubuntu-24.04-server-cloudimg-armhf.img"
arch: "armv7l"
digest: "sha256:e2e1780a3785482887ee61b05019a072c343e4dcff5fa5239e3a0696d44d117b"
- location: "https://cloud-images.ubuntu.com/releases/noble/release-20250704/ubuntu-24.04-server-cloudimg-s390x.img"
arch: "s390x"
digest: "sha256:f05c9c41ae23e82340799b0d04a0959b9e71e16526cd91f55188f531ce190c21"
- location: "https://cloud-images.ubuntu.com/releases/noble/release-20250704/ubuntu-24.04-server-cloudimg-ppc64el.img"
arch: "ppc64le"
digest: "sha256:7dc45587dac45028d022eaa56e102eca165dfd4b73fa294f8f2c447da4cc251a"
# Fallback to the latest release image.
# Hint: run `limactl prune` to invalidate the cache

- location: https://cloud-images.ubuntu.com/releases/noble/release/ubuntu-24.04-server-cloudimg-amd64.img
arch: x86_64

- location: https://cloud-images.ubuntu.com/releases/noble/release/ubuntu-24.04-server-cloudimg-arm64.img
arch: aarch64

- location: https://cloud-images.ubuntu.com/releases/noble/release/ubuntu-24.04-server-cloudimg-riscv64.img
arch: riscv64

- location: https://cloud-images.ubuntu.com/releases/noble/release/ubuntu-24.04-server-cloudimg-armhf.img
arch: armv7l

- location: https://cloud-images.ubuntu.com/releases/noble/release/ubuntu-24.04-server-cloudimg-s390x.img
arch: s390x

- location: https://cloud-images.ubuntu.com/releases/noble/release/ubuntu-24.04-server-cloudimg-ppc64el.img
arch: ppc64le

cpus: 4
memory: "8GiB"
disk: "20GiB"

```