Improve workspace root detection

[Hmbown]

Summary:\n- Resolve ALEPH_WORKSPACE_ROOT with PWD/INIT_CWD and expand ~.\n- Keep repo-root snapping while honoring env precedence.\n- Add tests for relative and tilde overrides.

[gemini-code-assist]

Summary of Changes

Hello @Hmbown, I'm Gemini Code Assist¹! I'm currently reviewing this pull request and will post my feedback shortly. In the meantime, here's a summary to help you and other reviewers quickly get up to speed!

This pull request significantly refines how the aleph system determines its workspace root, offering both greater control and improved reliability. By introducing an explicit environment variable (ALEPH_WORKSPACE_ROOT) and enhancing the automatic detection process to consider common invocation directories (PWD, INIT_CWD), it aims to resolve ambiguities and prevent path-related errors, ultimately providing a more stable and predictable environment for users.

Highlights

• Explicit Workspace Override: Introduced the ALEPH_WORKSPACE_ROOT environment variable, allowing users to explicitly define the workspace root. This variable supports relative paths and tilde expansion for greater flexibility.
• Enhanced Auto-Detection Logic: Improved the automatic workspace root detection mechanism to prioritize PWD and INIT_CWD environment variables before falling back to os.getcwd(). This ensures more accurate detection across various execution contexts.
• Path Resolution Fixes: Addressed issues where paths could 'escape' the workspace root, particularly when the server is initiated from an install path, by implementing robust resolution for environment-provided paths.
• Comprehensive Testing: Added new unit tests to validate the improved workspace root detection logic, covering scenarios such as relative path overrides via PWD/INIT_CWD and tilde expansion in ALEPH_WORKSPACE_ROOT.

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[gemini-code-assist]

Code Review

The pull request introduces significant improvements to workspace root detection by incorporating ALEPH_WORKSPACE_ROOT, PWD, and INIT_CWD environment variables, along with tilde expansion. This enhances flexibility and robustness in how the workspace root is determined. The changes are well-documented in CHANGELOG.md, MCP_SETUP.md, README.md, and docs/CONFIGURATION.md, and new tests have been added to cover the updated logic. The implementation is clean and correctly handles various scenarios for path resolution. I did not identify any issues that meet the criteria for medium, high, or critical severity.