Fix: Standardize outputs/ and improve GitHub token guidance

[tkstang]

Summary

This PR addresses two important consistency and usability issues:

1. Standardize on outputs/ directory across all skills
2. Add dual output (in-thread + file) to analysis skills
3. Improve GitHub token scope requirements for organization discovery

Changes

1. Directory Standardization

Before: Mixed use of generated/ (IC skills) and outputs/ (manager skills)
After: Consistent use of outputs/ everywhere

• ✅ Updated all IC skills to use <profile-root>/outputs/
• ✅ Updated AGENTS.md to reflect new structure
• ✅ Added clarifying comment to .gitignore
• ✅ Consistent paths across IC and manager modes

Files updated:

• AGENTS.md
• .gitignore
• 6 skill files

2. Dual Output for Analysis Skills

Problem: Skills like detect-projects, detect-themes, summarize-work only responded in-thread. Users had no persistent file to reference later.

Solution: All skills now do BOTH:

1. Respond in-thread (for MCP integration and immediate feedback)
2. Save to file in outputs/ (for persistence and future reference)

Skills updated:

• work-chronicler-detect-projects → outputs/projects-detected-YYYY-MM-DD.md
• work-chronicler-detect-themes → outputs/themes-detected-YYYY-MM-DD.md
• work-chronicler-summarize-work → outputs/work-summary-YYYY-MM-DD.md
• work-chronicler-generate-resume-bullets → outputs/resume-bullets-YYYY-MM-DD.md
• work-chronicler-write-self-review → outputs/self-review-YYYY-MM-DD.md
• work-chronicler-update-resume → outputs/resume-updated-YYYY-MM-DD.md

3. GitHub Token Scope Requirements

Problem: read:org scope requirement wasn't clear, causing auto-discovery to fail for organizations.

Solution:

• ✅ Updated README with clear scope requirements
• ✅ Updated token prompts in init wizard (IC and manager mode)
• ✅ Updated auto-discovery option description to mention read:org requirement
• ✅ Better error handling: detects INSUFFICIENT_SCOPES and shows helpful message

Example improved error:

GitHub token is missing the 'read:org' scope, which is required to query organizations.
Please add this scope at: https://github.com/settings/tokens

Files Changed

• Skills (6): Dual output + outputs/ paths
• Init (3): Better token guidance and error messages
• Docs (3): AGENTS.md, README.md, .gitignore

Testing

• Verified all skills mention dual output requirement
• Confirmed consistent use of outputs/ directory
• Tested init flow shows clear token requirements
• Error handling tested with missing read:org scope

Impact

• Better UX: Users get both immediate feedback AND persistent files
• Consistency: All skills use the same directory structure
• Clearer guidance: Token requirements are explicit and well-documented
• Better errors: Users know exactly what to fix when discovery fails