What
File sync keeps a folder on your machine and a cloud session's copy of your project in step. The message Claude Code shows when file sync stops has been rewritten. It now says nothing is removed on either side: the cloud session's checkout and your local folder both keep their files, and from then on they are separate copies. To move work between them you use git, the version control tool.
The old message said the cloud session would be told to empty its copy before Claude's next turn there.
Why
If the wording matches what Claude Code does, stopping sync no longer throws away the files in the cloud session. Any work you want to carry over between the two copies after that has to go through git.
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Only the message was seen to change; whether the cloud copy is actually no longer emptied is not confirmed.