feat: gitnexus integration

[YevheniiaLementova]

Summary

This PR integrates GitNexus as a first-class citizen of the Rosetta workspace initialization workflow by adding 3 gitnexus skills and repositioning the setup phase so documentation generation can detect and reference the code graph.

What Changed

Skill decomposition: 1 → 3

Skill	Responsibility
gitnexus-setup	Installation gate — runs analyze + setup, verifies MCP; used only at init time or on explicit user request
gitnexus-cli	CLI reference — maps analyze, status, clean, wiki, list commands to flags, effects, and when to run them
gitnexus-tools	MCP tool pattern-matching — maps user intent to the right gitnexus_* tool or resource (renamed from gitnexus-usage for clarity)

Worked examples moved out of the main SKILL.md body into gitnexus-tools/assets/gn-examples.md, loaded on-demand via ACQUIRE FROM KB to keep the core skill lean.

Phase reordering in init-workspace-flow

GitNexus setup moved from Phase 8 → Phase 6 (before the documentation phase). This allows the documentation phase to detect .gitnexus/ and automatically inject GitNexus usage guidance into CONTEXT.md. All downstream phases renumbered accordingly (9 total phases, unchanged structure).

Documentation auto-instrumentation

init-workspace-documentation SKILL.md now includes a special case: if .gitnexus/ exists, the skill appends a CONTEXT.md entry directing agents to use gitnexus-tools for graph-based code intelligence and gitnexus-cli for index management.

Safe indexing

npx gitnexus@latest analyze is now called with --skip-agents-md to prevent GitNexus from overwriting Rosetta-managed AGENTS.md and CLAUDE.md files during repository indexing.

[github-actions]

Rosetta Triage Review

Summary: This PR decomposes the monolithic gitnexus skill into three focused skills (gitnexus-setup, gitnexus-cli, gitnexus-usage), moves the GitNexus HITL phase from Phase 8 to Phase 6 (before documentation) in the init-workspace-flow, and systematically renumbers all downstream phases from 8 to 9 total.

Findings:

• ⚠️ XML tag mismatch in instructions/r3/core/skills/gitnexus-setup/SKILL.md: opening tag is <gitnexus_setup> (underscore) but closing tag is </gitnexus-setup> (hyphen) — inconsistent naming.
• ⚠️ Empty PR body — no description of motivation or rationale for the skill split and phase reordering. Please add context to help reviewers understand the why.
• ⚠️ Breaking change: gitnexus skill (renamed to gitnexus-setup) — existing workspaces that reference USE SKILL gitnexus`` will break. Any migration note or backward-compat alias should be considered.
• ℹ️ init-workspace-flow.md passes large-workspace-handling to phases 5, 7, 8 — verification (phase 9) is omitted. This mirrors old behavior (5, 6, 8) but worth confirming phase 9 does not also need the large-workspace hint.
• ✅ Phase renumbering is consistent and correctly propagated across all 9 workflow phase files.
• ✅ Architectural decision to run GitNexus phase before documentation (phase 6 → before phase 7) is sound — it allows the documentation skill to detect and reference the GitNexus index if present.
• ✅ New gitnexus-usage skill is comprehensive with worked examples covering debugging, exploration, impact analysis, and rename workflows.

Suggestions:

• Fix the XML tag mismatch: either use <gitnexus_setup>/</gitnexus_setup> or <gitnexus-setup>/</gitnexus-setup> consistently.
• Add a PR description explaining the motivation (e.g., why split into 3 skills, why move the phase order).
• Consider adding a note in docs/CONTEXT.md or a CHANGES entry about the gitnexus → gitnexus-setup rename for users upgrading existing workspaces.

Automated triage by Rosetta agent