fill: process skills before agents

[brunocunha00]

Summary

This PR updates the fill workflow to process skills before agents, so agent content can reference already-filled skills.

What Changed

• Updated fill target ordering to docs -> skills -> agents.
• Added skills support to context fill/list target enums in MCP and gateway types.
• Extended scaffolding fill tools to include skills in listings and pagination.
• Added recursive skills discovery in fill tooling to support nested skill layout (.context/skills//SKILL.md).
• Updated fill service validation to accept runs when only skills exist.
• Added/updated tests to verify:
  • fills work with only skills,
  • skills are processed before agents.

Files Changed

• src/services/fill/fillService.ts
• src/services/fill/fillService.test.ts
• src/services/ai/tools/fillScaffoldingTool.ts
• src/services/mcp/mcpServer.ts
• src/services/mcp/gateway/types.ts

Why

Agents should be generated with access to completed skill content. Previously, agents could be filled before skills were available in
the flow.

Validation

• npm run build ✅
• npm test -- src/services/fill/fillService.test.ts -- --runInBand ✅ (20 tests passing)

Notes

• This change preserves existing docs-first behavior while ensuring skills are available prior to agent fill.
• No breaking CLI command changes; this is ordering and target coverage improvement.