diff --git a/.claude/skills/gitnexus/gitnexus-cli/SKILL.md b/.claude/skills/gitnexus/gitnexus-cli/SKILL.md
index b73ea7ede..89d8f358a 100644
--- a/.claude/skills/gitnexus/gitnexus-cli/SKILL.md
+++ b/.claude/skills/gitnexus/gitnexus-cli/SKILL.md
@@ -19,6 +19,14 @@ node .gitnexus/run.cjs analyze
 
 Run from the project root. This parses all source files, builds the knowledge graph, writes it to `.gitnexus/`, and generates CLAUDE.md / AGENTS.md context files.
 
+> **These repos are AGENTS.md-only.** `analyze` always writes both context files and has no flag to suppress one. A root `CLAUDE.md` takes precedence over `AGENTS.md` in tools that read both, and the generated `CLAUDE.md` carries only the GitNexus block — so it would shadow the repo's actual conventions. Remove it after every `analyze`:
+>
+> ```bash
+> rm -f CLAUDE.md
+> ```
+>
+> It is gitignored, so it will not slip back into a commit.
+
 | Flag           | Effect                                                           |
 | -------------- | ---------------------------------------------------------------- |
 | `--force`      | Force full re-index even if up to date                           |
diff --git a/.gitignore b/.gitignore
index 9e25f627b..039f36caa 100644
--- a/.gitignore
+++ b/.gitignore
@@ -60,3 +60,8 @@ registry.json
 .antigravitycli/
 .pi/
 .coverage
+
+# Agent instructions: this repo is AGENTS.md-only.
+# `gitnexus analyze` regenerates a root CLAUDE.md that would shadow AGENTS.md
+# for tools that prefer it; keep the regenerated copy out of git.
+/CLAUDE.md
diff --git a/CLAUDE.md b/CLAUDE.md
deleted file mode 100644
index 7c0a695a2..000000000
--- a/CLAUDE.md
+++ /dev/null
@@ -1,44 +0,0 @@
-<!-- gitnexus:start -->
-# GitNexus — Code Intelligence
-
-This project is indexed by GitNexus as **graycode-skills** (210621 symbols, 225507 relationships, 136 execution flows). Use the GitNexus MCP tools to understand code, assess impact, and navigate safely.
-
-> Index stale? Run `node .gitnexus/run.cjs analyze` from the project root — it auto-selects an available runner. No `.gitnexus/run.cjs` yet? `npx gitnexus analyze` (npm 11 crash → `npm i -g gitnexus`; #1939).
-
-## Always Do
-
-- **MUST run impact analysis before editing any symbol.** Before modifying a function, class, or method, run `impact({target: "symbolName", direction: "upstream"})` and report the blast radius (direct callers, affected processes, risk level) to the user.
-- **MUST run `detect_changes()` before committing** to verify your changes only affect expected symbols and execution flows. For regression review, compare against the default branch: `detect_changes({scope: "compare", base_ref: "main"})`.
-- **MUST warn the user** if impact analysis returns HIGH or CRITICAL risk before proceeding with edits.
-- When exploring unfamiliar code, use `query({search_query: "concept"})` to find execution flows instead of grepping. It returns process-grouped results ranked by relevance.
-- When you need full context on a specific symbol — callers, callees, which execution flows it participates in — use `context({name: "symbolName"})`.
-- For security review, `explain({target: "fileOrSymbol"})` lists taint findings (source→sink flows; needs `analyze --pdg`).
-
-## Never Do
-
-- NEVER edit a function, class, or method without first running `impact` on it.
-- NEVER ignore HIGH or CRITICAL risk warnings from impact analysis.
-- NEVER rename symbols with find-and-replace — use `rename` which understands the call graph.
-- NEVER commit changes without running `detect_changes()` to check affected scope.
-
-## Resources
-
-| Resource | Use for |
-|----------|---------|
-| `gitnexus://repo/graycode-skills/context` | Codebase overview, check index freshness |
-| `gitnexus://repo/graycode-skills/clusters` | All functional areas |
-| `gitnexus://repo/graycode-skills/processes` | All execution flows |
-| `gitnexus://repo/graycode-skills/process/{name}` | Step-by-step execution trace |
-
-## CLI
-
-| Task | Read this skill file |
-|------|---------------------|
-| Understand architecture / "How does X work?" | `.claude/skills/gitnexus/gitnexus-exploring/SKILL.md` |
-| Blast radius / "What breaks if I change X?" | `.claude/skills/gitnexus/gitnexus-impact-analysis/SKILL.md` |
-| Trace bugs / "Why is X failing?" | `.claude/skills/gitnexus/gitnexus-debugging/SKILL.md` |
-| Rename / extract / split / refactor | `.claude/skills/gitnexus/gitnexus-refactoring/SKILL.md` |
-| Tools, resources, schema reference | `.claude/skills/gitnexus/gitnexus-guide/SKILL.md` |
-| Index, status, clean, wiki CLI commands | `.claude/skills/gitnexus/gitnexus-cli/SKILL.md` |
-
-<!-- gitnexus:end -->