False-positive warning when installing/updating with cache enabled

[noirbizarre]

• I have searched the issue tracker and believe that this is not a duplicate.

Make sure you run commands with -v flag before pasting the output.

Steps to reproduce

• Create a new PDM project
• Add any dependency to the n-1 version (eg. pytest==7.4.2)
• Lock & install
• Update dependency to the last version (eg. pytest==7.4.3)
• Lock & install

Actual behavior

Since #2359 PDM emit one warning by file or directory in each dependency he manages and update if caching is enabled.

$ pdm init -n    
Creating a pyproject.toml for PDM...
Virtualenv is created successfully at /tmp/demo/.venv
Project is initialized successfully

$ pdm add 'pytest==7.4.2'
Adding packages to default dependencies: pytest==7.4.2
🔒 Lock successful
Changes are written to pyproject.toml.
Synchronizing working set with resolved packages: 4 to add, 0 to update, 0 to remove

  ✔ Install iniconfig 2.0.0 successful
  ✔ Install pytest 7.4.2 successful
  ✔ Install packaging 23.2 successful
  ✔ Install pluggy 1.3.0 successful

🎉 All complete!

$ sed -i 's/7.4.2/7.4.3/' pyproject.toml

$ pdm install 

WARNING: Lockfile hash doesn't match pyproject.toml, packages may be outdated
Updating the lock file...
🔒 Lock successful
Changes are written to pdm.lock.
Synchronizing working set with resolved packages: 0 to add, 1 to update, 0 to remove

/home/noirbizarre/.local/pipx/venvs/pdm/lib/python3.11/site-packages/pdm/installers/installers.py:179: PDMWarning: Overwriting existing package: /tmp/demo/.venv/lib/python3.11/site-packages/_pytest
  for relpath in _create_links_recursively(
/home/noirbizarre/.local/pipx/venvs/pdm/lib/python3.11/site-packages/pdm/installers/installers.py:179: PDMWarning: Overwriting existing package: /tmp/demo/.venv/lib/python3.11/site-packages/pytest
  for relpath in _create_links_recursively(
  ✔ Update pytest 7.4.2 -> 7.4.3 successful

🎉 All complete!

Expected behavior

PDM only emit warning when replacing a flat dependency (file or directory) and is silent when replacing its own symlinks (it will still warn on the first time you install after enabling the cache)

$ pdm init -n    
Creating a pyproject.toml for PDM...
Virtualenv is created successfully at /tmp/demo/.venv
Project is initialized successfully

$ pdm add 'pytest==7.4.2'
Adding packages to default dependencies: pytest==7.4.2
🔒 Lock successful
Changes are written to pyproject.toml.
Synchronizing working set with resolved packages: 4 to add, 0 to update, 0 to remove

  ✔ Install iniconfig 2.0.0 successful
  ✔ Install pytest 7.4.2 successful
  ✔ Install packaging 23.2 successful
  ✔ Install pluggy 1.3.0 successful

🎉 All complete!

$ sed -i 's/7.4.2/7.4.3/' pyproject.toml

$ pdm install 

WARNING: Lockfile hash doesn't match pyproject.toml, packages may be outdated
Updating the lock file...
🔒 Lock successful
Changes are written to pdm.lock.
Synchronizing working set with resolved packages: 0 to add, 1 to update, 0 to remove

  ✔ Update pytest 7.4.2 -> 7.4.3 successful

🎉 All complete!

Environment Information

PDM version:
  2.11.1
Python Interpreter:
  /tmp/demo/.venv/bin/python (3.11)
Project Root:
  /tmp/demo
Local Packages:
  
{
  "implementation_name": "cpython",
  "implementation_version": "3.11.6",
  "os_name": "posix",
  "platform_machine": "x86_64",
  "platform_release": "6.6.6-arch1-1",
  "platform_system": "Linux",
  "platform_version": "#1 SMP PREEMPT_DYNAMIC Mon, 11 Dec 2023 11:48:23 +0000",
  "python_full_version": "3.11.6",
  "platform_python_implementation": "CPython",
  "python_version": "3.11",
  "sys_platform": "linux"
}