[BUG] Windows MSIX desktop app: Claude Code sessions inherit AppData filesystem virtualization, so tools installed from inside a session (uv Python, uv tools, caches) land in the package LocalCache and are invisible or broken outside the app

## What's Wrong?

The MSIX package `Claude_pzs8sxrjxfjjc` declares `virtualization:FileSystemWriteVirtualization` with only four excluded directories (`…\Microsoft\Office\16.0\WEF`, `…\Claude-3p`, `…\Claude-Data`, `…\Claude\logs`). Every descendant process of `Claude.exe` inherits that virtualization: the Claude Code CLI, its Bash/PowerShell tool shells, stdio MCP servers, and anything the user installs from a session.

Result: any write to `%APPDATA%` or `%LOCALAPPDATA%` made from inside a Claude Code session is silently redirected to `%LOCALAPPDATA%\Packages\Claude_pzs8sxrjxfjjc\LocalCache\{Roaming,Local}\…`. The env vars still show the normal paths, `Test-Path` succeeds inside the session, but a normal terminal sees nothing.

Concrete impact on my machine (verified with a probe file and with a helper spawned outside the package via WMI):

- `uv python install 3.11 3.13` and `uv tool install serena-agent`, run from Claude Code sessions, put ~400 MB of interpreters and venvs only inside the package LocalCache. `%APPDATA%\uv` did not exist for the rest of the system.
- uv's launcher shims in `~\.local\bin` (a non-virtualized path) embed `%APPDATA%\uv\python\cpython-3.13-windows-x86_64-none\python.exe`. Outside the app they fail with `uv trampoline failed to spawn Python child process: entity not found (os error 2)`. Inside the app they also fail (os error 3) because the minor-version directory is a junction whose target is the real, non-existent path.
- The Serena MCP server registered in `~/.claude.json` therefore only worked when launched by the desktop app; `serena --version` in a normal terminal failed with `failed to canonicalize script path`.
- A user with `pip`, `npm` caches, `cargo`, `dotnet tool`, etc. would hit the same split-brain state without any error message.

## What Should Happen?

Processes spawned for Claude Code sessions should see the same filesystem as the user's other terminals. Options:

- Disable `FileSystemWriteVirtualization` (and `RegistryWriteVirtualization`) for the package, as most developer-tool MSIX packages do, or
- Exclude `%APPDATA%` / `%LOCALAPPDATA%` broadly for child processes, or spawn the CLI through a non-virtualized broker (the package already ships an out-of-package service, `cowork-svc.exe`), or
- At minimum, document the behaviour prominently and warn when a session writes under AppData.

## Error Messages/Logs

Probe from inside a session (PowerShell tool):

```
wrote: C:\Users\\AppData\Roaming\uv\.virt-probe.txt
physical? C:\Users\\AppData\Local\Packages\Claude_pzs8sxrjxfjjc\LocalCache\Roaming\uv\.virt-probe.txt -> True
```

Same paths from a process created with `Invoke-CimMethod Win32_Process Create` (outside the package):

```
--- REAL C:\Users\\AppData\Roaming\uv : (ABSENT)
--- REAL C:\Users\\AppData\Local\uv : (ABSENT)
python3.13.exe : error: uv trampoline failed to spawn Python child process
Caused by: entity not found (os error 2)
serena.exe : error: uv trampoline failed to canonicalize script path
uv.exe : No tools installed
```

Manifest excerpt (`C:\Program Files\WindowsApps\Claude_1.49585.0.0_x64__pzs8sxrjxfjjc\AppxManifest.xml`):

```xml

$(KnownFolder:LocalAppData)\Microsoft\Office\16.0\WEF
$(KnownFolder:LocalAppData)\Claude-3p
$(KnownFolder:LocalAppData)\Claude-Data
$(KnownFolder:LocalAppData)\Claude\logs

```

## Steps to Reproduce

1. Install Claude Desktop from the Microsoft Store (MSIX) on Windows 11.
2. In a Code-tab session, run `New-Item "$env:APPDATA\probe.txt"` (or `uv python install 3.13`).
3. In a regular Windows Terminal: `Test-Path "$env:APPDATA\probe.txt"` → False. The file is at `%LOCALAPPDATA%\Packages\Claude_pzs8sxrjxfjjc\LocalCache\Roaming\probe.txt`.

## Claude Code Version

Desktop app 1.49585.0.0 (MSIX); bundled Claude Code 2.1.260.

## Platform

Claude.ai subscription (OAuth) via the desktop app.

## Operating System

Windows 11 Pro 10.0.26200.

## Terminal/Shell

Desktop app Bash and PowerShell tools; reproduced in both.

## Additional Information

Workaround I applied: pin tool state outside AppData with user env vars (`UV_PYTHON_INSTALL_DIR`, `UV_TOOL_DIR` → `~\.local\share\uv\…`, `UV_CACHE_DIR` → `~\.cache\uv`), reinstall, and delete the LocalCache copies. `HKCU\Environment` writes from inside a session are not virtualized, so the env vars took effect after an app restart.

Start with the installed AppxManifest.xml and the Claude Code session entry points that launch Claude.exe, Bash, PowerShell, and stdio MCP servers. Reproduce the PowerShell AppData probe and an external-terminal check, then determine which listed virtualization or broker option makes session writes visible to normal terminals. Done means uv installs, caches, and MCP tools work consistently inside and outside the desktop app.

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