fix(core): prefer nearest skill source - #41788

What

Ensure duplicate discovered skill IDs resolve to the source nearest the session directory. In a nested git worktree, the worktree copy now wins over a farther parent checkout copy, keeping the selected skill on the checked-out branch and inside the session directory.

Closes #39871

Before / After

Before: Config ancestor discovery returned nearby .agents and .claude directories first. The skill plugin applies later-source precedence, so a duplicate skill from the farther parent checkout replaced the worktree copy and could trigger an external_directory permission request.

After: Discovered .agents and .claude directories are ordered from farthest to nearest. Existing later-source precedence deterministically selects the nearest duplicate skill, including its local SKILL.md location.

How

• Order ancestor .agents and .claude config entries from low to high priority, consistent with direct config and .opencode discovery.
• Add a filesystem regression shaped like a parent checkout and nested linked worktree, with duplicate skill IDs in both locations.
• Update the existing cross-project-boundary config assertion to reflect the corrected source priority.

Scope

This preserves the cross-git/project-boundary ancestor discovery introduced by #36577. It does not restore a git-root stop boundary: farther parent checkout config and skills are still discovered when no nearer source overrides them.

Testing

• bun run test test/config/skill.test.ts from packages/core (9 passed)
• bun run test test/config/config.test.ts from packages/core (33 passed)
• bun typecheck from packages/core (passed)
• Pre-push bun turbo typecheck --concurrency=3 (33 tasks passed)
• bunx prettier --check src/config.ts test/config/config.test.ts test/config/skill.test.ts from packages/core (passed)

The new regression was run before the implementation change and failed with Expected: "Worktree", Received: "Parent checkout"; it passes after the fix.