CLI: make AGENTS-relative skill paths unambiguous when cwd is a nested checkout

Summary

When an active AGENTS.md refers to a project-installed skill as .agents/skills/<name>/SKILL.md, an agent running from a nested checkout can incorrectly resolve that path against its process cwd instead of the directory that contains the applicable AGENTS.md.

Reproduction

1. Arrange a workspace as follows:

workspace/
├── AGENTS.md
├── .agents/skills/beads/SKILL.md
└── checkout/

2. Start Codex with workspace/checkout as the cwd while the parent workspace/AGENTS.md is active.
3. Have AGENTS.md direct the agent to load .agents/skills/beads/SKILL.md.

Actual behavior

The relative path is easy to interpret as workspace/checkout/.agents/..., which does not exist, even though the skill registry exposes the canonical absolute skill location.

Expected behavior

Codex should expose an unambiguous canonical origin for every active AGENTS.md and canonical absolute paths for registered skills, or document/enforce that paths referenced by AGENTS.md are resolved relative to that file rather than cwd. This prevents unnecessary failed filesystem probes and makes project-level skill discovery deterministic.

Suggested direction

A codex debug agents-md/skill-resolution view could report the instruction-file origin and the resolved path for each referenced project skill.

Start by tracing AGENTS.md discovery and project-skill resolution from the CLI, then reproduce the nested-checkout layout with workspace/checkout as cwd. Done means the instruction-file origin and registered skill paths are unambiguous, either through canonical output such as a debug view or documented enforcement of resolution relative to AGENTS.md.