Kart does not see changes when a tracked table in a geopackage working copy is replaced by geopandas

**Describe the bug** When re-creating a kart tracked (geopackage working copy) table using geopandas (python), kart sees no changes, and doesn't see the table as an untracked table either. This is tricky since it's easy to miss if you have other changes commited at the same time, and assume that your changes were stored. The table structure is the same before and after, as is the name. My guess is that something kart is using to track if changes have happened at a coarse level is not triggering, since in this case the geometry of every row has changed. I can work around it by deleting the table, comitting that, and re-importing it, but that's tedious and easy to miss. **To Reproduce** Steps to reproduce the behaviour: 1. Have a geopackage working copy with a geometry layer/table (for example "foo" containing linestrings. 2. Replace the layer contents with: ``` gdf = geopandas.GeoDataFrame.from_features(feature_collection, crs="EPSG:22817") gdf.to_file(output_file, layer="foo", driver="GPKG") ``` 3. Run `kart status` **Expected behaviour** What did you expect to happen? Kart should show changes based on the delta of the tables (e.g. X rows deleted, Y rows added etc. **Output** `Nothing to commit, working copy clean` **Version Info ** - OS: Ubuntu 24.04 - Version: ``` kart --version Kart v0.16.1, Copyright (c) Kart Contributors » GDAL v3.8.5; PROJ v9.4.0; PDAL v2.7.2 » PyGit2 v1.12.1; Libgit2 v1.6.4; Git v2.47.1; Git LFS v3.3.0 » SQLAlchemy v1.4.45; pysqlite3 v2.6.0/v3.45.3; SpatiaLite v5.1.0; Libpq v16.0.2 Executed via helper, SID=644898 PID=900309 ```