Multiple project roots not configured when one root is a subdirectory of the other

### Brief Issue Summary

When there are two paths in `sourceDirectory`, and one of them is a subdirectory of the other, only the higher-level project root is configured by CMake Tools. An example repo is here for reproduction: https://github.com/harrymander/vscode-cmake-tools-nested-roots

```
.
├── CMakeLists.txt # calls cmake `project` command, does not add `nested` directory
├── main.cpp
└── nested
├── CMakeLists.txt # calls cmake `project` command
└── main-nested.cpp
```

I have the following in my `settings.json`:

```json
"cmake.sourceDirectory": ["${workspaceFolder}", "${workspaceFolder}/nested"]
```

However, only the top-level project is configured by CMake Tools. When I open `nested/CMakeLists.txt` and run `CMake: Configure` from the command palette, it just configures the top-level project, creating a build directory under `${workspaceFolder}/build`, when I would expect it to configure a new CMake root under `${workspaceFolder}/nested/build`.

The problem is not present if I move the cross-compiling cmake project to a subdirectory.

### CMake Tools Diagnostics

```shell
{
"os": "linux",
"vscodeVersion": "1.88.1",
"cmtVersion": "1.17.17",
"configurations": [
{
"folder": "/home/harry/scratch/vscode-cmake-tools-nested-roots",
"cmakeVersion": "unknown",
"configured": false,
"generator": "unknown",
"usesPresets": false,
"compilers": {}
},
{
"folder": "/home/harry/scratch/vscode-cmake-tools-nested-roots/nested",
"cmakeVersion": "unknown",
"configured": false,
"generator": "unknown",
"usesPresets": false,
"compilers": {}
}
],
"cpptoolsIntegration": {
"isReady": false,
"hasCodeModel": false,
"activeBuildType": "",
"buildTypesSeen": [],
"requests": [],
"responses": [],
"partialMatches": [],
"targetCount": 0,
"executablesCount": 0,
"librariesCount": 0,
"targets": []
},
"settings": [
{
"communicationMode": "automatic",
"useCMakePresets": "auto",
"configureOnOpen": null
},
{
"communicationMode": "automatic",
"useCMakePresets": "auto",
"configureOnOpen": null
}
]
}
```

### Debug Log

```shell
[expand] expanding cmake
[main] Configuring project: vscode-cmake-tools-nested-roots
[main] Saving open files before configure/build
[expand] expanding /home/harry/scratch/vscode-cmake-tools-nested-roots
[expand] expanding ${sourceDirectory}/build
[driver] Start configure
[driver] Running pre-configure checks and steps
[driver] Using compilers in GCC 11.3.0 x86_64-linux-gnu for configure
[expand] expanding --no-warn-unused-cli
[expand] expanding -DCMAKE_BUILD_TYPE:STRING=Debug
[expand] expanding -DCMAKE_EXPORT_COMPILE_COMMANDS:BOOL=TRUE
[expand] expanding -DCMAKE_C_COMPILER:FILEPATH=/usr/bin/gcc
[expand] expanding -DCMAKE_CXX_COMPILER:FILEPATH=/usr/bin/g++
[expand] expanding /home/harry/scratch/vscode-cmake-tools-nested-roots
[expand] expanding ${sourceDirectory}/build
[cmakefileapi-driver] Configuring using kit
[cmakefileapi-driver] Invoking CMake /usr/bin/cmake with arguments ["--no-warn-unused-cli","-DCMAKE_BUILD_TYPE:STRING=Debug","-DCMAKE_EXPORT_COMPILE_COMMANDS:BOOL=TRUE","-DCMAKE_C_COMPILER:FILEPATH=/usr/bin/gcc","-DCMAKE_CXX_COMPILER:FILEPATH=/usr/bin/g++","-S/home/harry/scratch/vscode-cmake-tools-nested-roots","-B/home/harry/scratch/vscode-cmake-tools-nested-roots/build","-G","Ninja"]
[proc] Executing command: /usr/bin/cmake --no-warn-unused-cli -DCMAKE_BUILD_TYPE:STRING=Debug -DCMAKE_EXPORT_COMPILE_COMMANDS:BOOL=TRUE -DCMAKE_C_COMPILER:FILEPATH=/usr/bin/gcc -DCMAKE_CXX_COMPILER:FILEPATH=/usr/bin/g++ -S/home/harry/scratch/vscode-cmake-tools-nested-roots -B/home/harry/scratch/vscode-cmake-tools-nested-roots/build -G Ninja
[proc] with environment: 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[cmake] Not searching for unused variables given on the command line.
[cmake] -- The CXX compiler identification is GNU 11.4.0
[cmake] -- Detecting CXX compiler ABI info
[cmake] -- Detecting CXX compiler ABI info - done
[cmake] -- Check for working CXX compiler: /usr/bin/g++ - skipped
[cmake] -- Detecting CXX compile features
[cmake] -- Detecting CXX compile features - done
[cmake] -- Configuring done
[cmake] -- Generating done
[cmake] -- Build files have been written to: /home/harry/scratch/vscode-cmake-tools-nested-roots/build
[cmakefileapi-parser] Read reply folder: /home/harry/scratch/vscode-cmake-tools-nested-roots/build/.cmake/api/v1/reply
[cmakefileapi-parser] Found index files: ["cache-v2-d48585cc9578518c162f.json","cmakeFiles-v1-bc10beb90439ca5d24af.json","codemodel-v2-f231b8cc75d3d7843591.json","directory-.-Debug-f5ebdc15457944623624.json","index-2024-04-21T02-04-55-0449.json","target-main-Debug-19b5de53e7aaa2ef28f9.json","toolchains-v1-a2904c2398fb9530b017.json"]
[expand] expanding cmake
[extension] [6414] cmake.configure finished (returned 0)
[expand] expanding cmake
[cache] Reading CMake cache file /home/harry/scratch/vscode-cmake-tools-nested-roots/build/CMakeCache.txt
[cache] Parsing CMake cache string
[expand] expanding cmake
```

### Additional Information

_No response_

Reproduce the issue with the linked nested-roots example, using settings.json with the two cmake.sourceDirectory entries and the top-level and nested CMakeLists.txt files. Start with the CMake: Configure command and compare the diagnostics and debug log; done means selecting nested/CMakeLists.txt configures a separate nested/build directory without changing the top-level behavior.

Written by the indexing model from the issue text.