VFS: Regression in Union FS: Excessive copying of files

[theduke]

The new union FS implementation leads to excessive copying of files into the host file system, delaying startup significantly and causing lots of extra work.

To reproduce:

RUST_LOG=virtual_fs=trace,wasmer_wasix=trace wasmer run --registry wasmer.wtf  --net sha256:68c1f418474d98f0c4ca44d6754f144fe355525d1ba347dc52ab934cb98c5dad &| tee log.txt &

curl localhost:8080

❯ cat log.txt | grep 'Copying file into host filesystem' | wc -l
5846

This might also cause some kind of deadlocking or freezes, as seen in the app above.
The PHP code stalls and the request never returns.