pnpm-workspace allowBuilds reset on aspire run

### Is there an existing issue for this?

- [x] I have searched the existing issues

### Describe the bug

When trying to run `aspire run`, `allowBuilds` in `pnpm-workspace.yaml` often (~50% of time) reset to default `set this to true or false`. This should only happen the first time a build script is executed on newer version of pnpm.

### Expected Behavior

Once set, `pnpm-workspace.yaml` should stay unchanged. New script should be appended at the end like it is usually the case

### Steps To Reproduce

https://github.com/[maxime-louellette/aspire-pnpm-workspace-repro-issue](https://github.com/maxime-louellette/aspire-pnpm-workspace-repro-issue)

- npm add -g pnpm@11.5.2
- replace `set this to true or false` with `true` in `pnpm-worspace.yaml`
- aspire run
- exit process
- aspire run

You can repeat the last 2 step until it reproduce

### Exceptions (if any)

```
[ERR_PNPM_IGNORED_BUILDS] Ignored build scripts: esbuild@0.28.0, protobufjs@7.6.2
```

full log
https://github.com/maxime-louellette/aspire-pnpm-workspace-repro-issue/blob/main/logs/cli_20260608T143700_58ec751e.log

### Aspire doctor output

Aspire Environment Check
========================

Aspire
✅ Aspire CLI version 13.4.2 (channel: stable)

AppHost
✅ AppHost version 13.4.2 (channel: stable) (apphost.mts)

Container Runtime
✅ Docker v29.2.1: running (auto-detected (default)) ← active

Environment
✅ TypeScript AppHost tooling found (pnpm).
⚠️ Multiple HTTPS development certificates found (2 certificates)
Run 'aspire certs clean' to remove all certificates, then run 'aspire certs trust' to create and trust a new one.
See: https://aka.ms/aspire-prerequisites#dev-certs
Details:
Found certificates: v6 (9B7460A5...) [trusted], v4 (155F2515...). Having multiple certificates can cause confusion when selecting which one to use.

Summary: 4 passed, 1 warnings, 0 failed
For detailed prerequisites: https://aka.ms/aspire-prerequisites

Aspire CLI Installations
========================

╭──────────────────────────────────────────────────────────────────────────┬─────────────────────────────────────────────────┬──────────────┬──────────────┬─────────────╮
│ Path │ Version │ Channel │ Route │ PATH status │
├──────────────────────────────────────────────────────────────────────────┼─────────────────────────────────────────────────┼──────────────┼──────────────┼─────────────┤
│ C:\Users\myusername\.aspire\npm\13.4.2\win-x64\bin\aspire.exe (current) │ 13.4.2+d7d0b6759ce4b936c76bc4775814d27db560dd6d │ stable │ (unknown) │ not on PATH │
│ C:\Users\myusername\AppData\Roaming\npm\aspire.CMD │ (not probed) │ (not probed) │ (not probed) │ active │
╰──────────────────────────────────────────────────────────────────────────┴─────────────────────────────────────────────────┴──────────────┴──────────────┴─────────────╯
Waiting for the debugger to disconnect...

### Anything else?

pnpm version 11.5.2, but this is related to changes since pnpm v11 that force approval of build script.

This is a monorepo using typescript and pnpm

Development is in VSCode

This behaviour only occur about half the time. the pnpm-workspace change does not happen half of the time.