Fixes #3978

Problem
pi config grouped auto-discovered skills from ~/.agents/skills under User (~/.pi/agent/) because both directories received identical metadata (baseDir: ~/.pi/agent, source: "auto"). The same issue existed for project .agents/skills.

Root Cause
In addAutoDiscoveredResources(), all auto-discovered skills were flattened into single addResources() calls before assigning metadata, losing provenance information about which root directory each skill came from.

Changes

packages/coding-agent/src/core/package-manager.ts:

• Split auto-discovered skill handling to preserve provenance
• User ~/.agents/skills now gets baseDir: ~/.agents (was ~/.pi/agent)
• Each project .agents/skills directory gets its own baseDir pointing to its parent .agents dir
• Skills from .pi directories continue to use their .pi baseDir as before

packages/coding-agent/src/modes/interactive/components/config-selector.ts:

• Added baseDir to group key to prevent collapsing different sources
• Added cross-platform formatBaseDir() helper that normalizes Windows backslashes
• Updated group labels to show actual baseDir (e.g., User (~/.agents/))

packages/coding-agent/test/package-manager.test.ts:

• Added HOME environment mocking to symlink test to prevent interference from real ~/.agents directory

Verification

• All 99 package-manager tests pass
• npm run check passes (lint, format, typecheck)
• Four new tests verify correct metadata assignment for each skill source type