Worktree changes not saved

When agent works in a worktree and writes to a file, the changes are not actually saved on the disk.
In the screenshot below agent created new files: Organization and CurrencyConverter and modified User file. On disk both organization and currencyconverter files are empty and user file does not contain the changes agent made.
I must go through all the changed files, save them manually and then the files are modified on the disk.
The problem is when agent tries to run a test in the worktree, it fails because no changes are actually there, unless I manually save them.
I believe this should not be the case.

image

Version: 2.1.0-pre.2.patch.0 (user setup)
VSCode Version: 1.99.3
Commit: d3c12e88360374a70d1a6729bae06ca5444bb080
Date: 2025-11-02T08:14:12.227Z
Electron: 37.7.0
Chromium: 138.0.7204.251
Node.js: 22.20.0
V8: 13.8.258.32-electron.0
OS: Windows_NT x64 10.0.19045

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also when i click “apply all changes”, not all files are copied from worktree into the main project folder