Error running 'main.dart': Entrypoint isn't within a Flutter pub root

Hi,

I cannot run flutter from intellij because of the following error:

```
Error running 'main.dart':
Entrypoint isn't within a Flutter pub root
```

Flutter doctor:

```
[✓] Flutter (Channel stable, 3.44.6, on Fedora Linux 44 (Workstation Edition) 7.0.14-201.fc44.x86_64, locale fr_FR.UTF-8) [43ms]
• Flutter version 3.44.6 on channel stable at
• Upstream repository https://github.com/flutter/flutter.git
• Framework revision ee80f08bbf (il y a 12 jours), 2026-07-08 15:02:06 -0700
• Engine revision 83675ed276
• Dart version 3.12.2
• DevTools version 2.57.0
• Feature flags: enable-web, no-enable-linux-desktop, enable-macos-desktop, enable-windows-desktop, enable-android, enable-ios, cli-animations, enable-native-assets, enable-swift-package-manager,
omit-legacy-version-file, enable-lldb-debugging, enable-uiscene-migration

[✓] Android toolchain - develop for Android devices (Android SDK version 36.1.0) [7,3s]
• Android SDK at
• Emulator version 36.6.11.0 (build_id 15507667) (CL:N/A)
• Platform android-36, build-tools 36.1.0
• Java binary at: /usr/bin/java
This JDK was found in the system PATH.
To manually set the JDK path, use: `flutter config --jdk-dir="path/to/jdk"`.
• Java version OpenJDK Runtime Environment Temurin-21.0.11+10 (build 21.0.11+10-LTS)
• All Android licenses accepted.

[✗] Chrome - develop for the web (Cannot find Chrome executable at google-chrome) [9ms]
! Cannot find Chrome. Try setting CHROME_EXECUTABLE to a Chrome executable.

[✓] Connected device (1 available) [134ms]
• Pixel 8 (mobile)

[✓] Network resources [210ms]
• All expected network resources are available.

! Doctor found issues in 1 category.
```

Dart plugin version is 507.0.0
Flutter plugin version is 94.0.0
IntelliJ version is IntelliJ IDEA 2026.2

## Workaround

Found in https://github.com/flutter/flutter-intellij/issues/4692#issuecomment-4660820365 : delete `lib/.dart_tool` folder

Reproduce the IntelliJ run of main.dart using the reported Flutter, Dart, and plugin versions, then compare the project state before and after deleting lib/.dart_tool. Trace how the plugin handles that directory and project-root detection; done means the entrypoint runs without requiring that workaround.

Written by the indexing model from the issue text.