Workspace status and checks misclassify in-workspace repository symlinks

[codeforester]

Goal

Make manifest-backed workspace reports preserve logical repository names and apply one consistent workspace-root boundary policy to symlinked paths.

Background

workspace_manifest_entries() retains the logical candidate path, but the manifest status and check aggregators index entries by entry.path.parent.resolve().name. For workspace/api -> workspace/physical with a manifest entry named api, a healthy repository is reported as missing under api and as an unlisted extra under physical.

The read-only report paths also do not reuse the containment resolver used by workspace mutation paths, so an outside-resolving symlink is not handled consistently. This was reproduced on origin/main 734a458a: one healthy in-root symlink produced an expected api missing result plus an extra physical warning.

Scope

• Workspace scanner, status, check, and shared path metadata
• Workspace doctor, onboarding, and agent-brief consumers
• Regression tests and user-facing documentation for in-root and outside-resolving symlinks

Acceptance Criteria

• A manifest entry is matched by its logical repository name when the repository directory is an in-workspace symlink.
• status, check, doctor, onboarding, and agent-brief report one expected repository with the logical name and do not invent a physical-name extra.
• Outside-resolving symlinks follow the workspace containment policy and are not inspected as undeclared in-workspace repositories.
• Regular directories, bare repositories, undeclared repositories, and existing extra detection retain their current behavior.
• Focused tests cover in-root and outside-resolving symlinks for every affected read-only consumer.

Validation

• python -m pytest cli/python/base_projects/tests/test_workspace_status_manifest.py cli/python/base_projects/tests/test_workspace_checks.py cli/python/base_projects/tests/test_workspace_onboarding.py cli/python/base_projects/tests/test_workspace_agent_brief.py -q
• env -u BASE_HOME ./bin/base-test
• git diff --check

Non-Goals

• No change to clone, update, configure, or setup mutation semantics already covered by containment tests.
• No recursive workspace discovery.

Project Fields

• Status: Backlog
• Priority: P1
• Area: Workspace
• Initiative: Workspace Handling
• Size: S
• Milestone: v1.10.0

Agent Assignment

• Human first; the read-only report contract and symlink boundary need maintainer review before implementation.