feat: Separate custom skills into .agents/skills-custom/ with dedicated manifest section

[Copilot]

All skills previously lived flat in .agents/skills/, making it impossible to .gitignore auto-managed framework skills while committing project-specific ones.

Changes

New directory structure

• .agents/skills/ — framework/core skills, auto-managed by CLI (safe to .gitignore)
• .agents/skills-custom/ — project-authored skills (should be committed)

# Recommended .gitignore strategy
.agents/**
!.agents/
!.agents/manifest.json
!.agents/guidelines/
!.agents/guidelines/custom/**
!.agents/skills-custom/
!.agents/skills-custom/**

Manifest

• Added customSkills: [] as a separate top-level key — not SHA-hash-managed (no owner/repo/sha tracking)
• skills[] now contains only remote-fetched framework skills
• Backwards-compatible: refresh() initializes customSkills on old manifests

SkillManager

• getCustomSkillsDirectory() — returns .agents/skills-custom/
• getCustomSkillFilePath() — custom-only lookup
• ensureCustomSkillsSection() — private helper for backwards-compat initialization
• createCustomSkill() / createSkillOverride() — write to skills-custom/, record in manifest.customSkills
• getSkillFilePath() — searches skills/, then skills-custom/, then .claude/skills/
• hasSkill() / removeSkillFromProject() — check/operate on both directories
• refresh() step 4/5 — prune deleted custom skills from customSkills, scan skills-custom/ for untracked new entries
• diagnose() — validates both skills and customSkills manifest sections

AIService

• Creates skills-custom/ in createAIDirectoryStructure()
• getInfo() returns customSkills; getStats() counts and sizes both directories

Commands & templates

• create, override commands use skills-custom/
• list command groups and totals from both info.skills + info.customSkills
• Agent instruction templates updated to document the two-directory structure with correct paths