Reproduction steps:
1. Create a new Unity project
2. Install the “com.unity.terrain-tools” package through the Package Manager
3. Observe the Console Window

Expected result: No warning related to the meta data file
Actual result: The warning “A meta data file (.meta) exists but its folder 'Packages/com.unity.terrain-tools/Editor/Icons/TerrainOverlays/ToolModeIcons' can't be found, and has been created. Empty directories cannot be stored in version control, so it's assumed that the meta data file is for an empty directory in version control. When moving or deleting folders outside of Unity, please ensure that the corresponding .meta file is moved or deleted along with it” is shown

Reproducible with: 5.1.0-pre.1, 5.1.0 , 5.1.1 (6000.0.1f1)
Not reproducible with: 4.0.5 (2021.3.38f1), 5.0.4 (2022.3.28f1)

Reproduced on: Windows 11 23H2 (22631.3007), Windows 10 (10.0.19045) 64bit (user’s)
Not reproduced on: No other environment tested

Note: To reproduce with the attached project remove and reinstall the “com.unity.terrain-tools” package in the project.