fix(project): use directory root for non-git projects

[lin-hongkuan]

Issue for this PR

Closes #24694

Type of change

• Bug fix
• New feature
• Refactor / code improvement
• Documentation

What does this PR do?

When ProjectV2.resolve() returns no VCS, Project.fromDirectory() was using / as the global project worktree/sandbox. That makes tool permission paths relative to the filesystem root, so a project file such as src/secret.ts can be checked as a long root-relative path fragment instead of the project-relative rule users configured.

This keeps git behavior unchanged, but normalizes the opened directory once and uses it as the non-git worktree/sandbox. containsPath() keeps its / guard for legacy persisted rows so old data cannot make the filesystem root count as in-project.

Regression coverage now checks that:

• Project.fromDirectory() returns the opened directory for non-git worktree/sandbox.
• InstanceStore.load() exposes the opened directory as the non-git instance worktree.
• Read permission requests in non-git projects use project-relative paths like src/secret.ts.

How did you verify your code works?

• bun test test/project/project.test.ts
• bun test test/project/instance.test.ts
• bun test test/tool/read.test.ts
• bun run typecheck
• git diff --check

Screenshots / recordings

Not applicable, no UI change.

Checklist

• I have tested my changes locally
• I have not included unrelated changes in this PR