fix(installer): stop duplicating agent instructions; MCP server is the single source of truth (#529) (#538)

The installer wrote a `## CodeGraph` usage block into each agent's
instructions file (CLAUDE.md / AGENTS.md / GEMINI.md / .cursor/rules /
Kiro steering) that duplicated, almost verbatim, the guidance the MCP
server already emits in its `initialize` response — so agents that
surface MCP instructions (Claude Code) read the same playbook twice
every turn.

All 6 instruction-writing targets (claude, cursor, codex, opencode,
gemini, kiro) now stop writing the block. install self-heals by
stripping a block a previous version wrote (uninstall already did), so
the next `codegraph install`/`uninstall` cleans up existing installs;
upgrading the package alone does not (the leftover block is harmless).
server-instructions.ts is now the single source of truth — the two
steers unique to the old template ("trust codegraph, don't re-verify
with grep" and the not-initialized -> `init -i` hint) are ported there.

Removes the now-dead INSTRUCTIONS_TEMPLATE / CLAUDE_MD_TEMPLATE,
claude-md-template.ts, writeClaudeMd / hasClaudeMdSection, and the
Cursor-only wireProjectSurfaces bootstrap. The install log learned a
"Removed" verb. Tests rewritten to the new contract + self-heal
coverage (140/140 installer tests pass).

Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

CLAUDE.md

@@ -74,12 +74,11 @@ Defined in `src/types.ts`. Both extractors and resolvers must use these exact st
 `src/installer/` is the entry point for `codegraph install` (and the bare `codegraph`/`npx @colbymchenry/codegraph` invocation). Architecture:
 
 - `targets/registry.ts` lists every supported agent.
-- `targets/types.ts` defines the `AgentTarget` interface — adding a 5th agent (Continue, Zed, Windsurf…) is **one new file in `targets/` + one entry in `registry.ts`**. Each target owns its config-file location, MCP-server JSON/TOML/JSONC writing, and instructions-file path.
+- `targets/types.ts` defines the `AgentTarget` interface — adding a 5th agent (Continue, Zed, Windsurf…) is **one new file in `targets/` + one entry in `registry.ts`**. Each target owns its config-file location and MCP-server JSON/TOML/JSONC writing. (Targets no longer write an instructions file — see below.)
 - Current targets: `claude.ts`, `cursor.ts`, `codex.ts`, `opencode.ts`.
 - `targets/toml.ts` is a hand-rolled TOML serializer scoped to `[mcp_servers.codegraph]` (used by Codex). Sibling tables and `[[array_of_tables]]` are preserved verbatim. No new dependency.
 - opencode reads `opencode.jsonc` by default; the installer prefers existing `.jsonc`, falls back to `.json`, and creates `.jsonc` for greenfield installs. Edits are surgical via `jsonc-parser` so user comments and formatting survive install/re-install/uninstall round-trips.
-- `instructions-template.ts` is the agent-agnostic instructions file written to each target (e.g. `CLAUDE.md`, `.cursor/rules/codegraph.mdc`, `~/.codex/AGENTS.md`, `~/.config/opencode/AGENTS.md`). It explicitly says "trust codegraph results, don't re-verify with grep" — earlier versions prescribed Claude-specific "spawn an Explore agent" and confused other agents.
-- `claude-md-template.ts` is the legacy Claude-only template, retained for compatibility paths.
+- `instructions-template.ts` no longer holds an instructions body — it exports only the `<!-- CODEGRAPH_START -->`/`<!-- CODEGRAPH_END -->` markers. The installer **stopped writing** a `## CodeGraph` block into each agent's instructions file (`CLAUDE.md` / `~/.codex/AGENTS.md` / `~/.config/opencode/AGENTS.md` / `~/.gemini/GEMINI.md` / `.cursor/rules/codegraph.mdc` / Kiro steering doc) because it duplicated the MCP `initialize` instructions verbatim (issue #529). Each target's `install` (self-heal on upgrade) and `uninstall` use the markers to **strip** a block a previous install left behind. `server-instructions.ts` is the single source of truth for agent-facing guidance.
 - All installer changes need matching coverage in `__tests__/installer-targets.test.ts` — there are ~47 parameterized contract tests covering install idempotency, sibling preservation, uninstall reverses install, byte-equal re-runs returning `unchanged`, and partial-state recovery for Codex.
 
 ### Cursor MCP working-directory quirk
@@ -88,7 +87,7 @@ Cursor launches MCP subprocesses with the wrong cwd and doesn't pass `rootUri` i
 
 ### MCP server instructions
 
-`src/mcp/server-instructions.ts` is sent back to the agent in the MCP `initialize` response. This is the *first* thing every agent sees about how to use the tools — treat it as the authoritative tool guidance and keep it in sync with `instructions-template.ts` and `.cursor/rules/codegraph.mdc`.
+`src/mcp/server-instructions.ts` is sent back to the agent in the MCP `initialize` response. This is the *first* thing every agent sees about how to use the tools, and as of issue #529 it is the **single source of truth** for agent-facing tool guidance — the installer no longer writes a duplicate `## CodeGraph` instructions block into `CLAUDE.md` / `AGENTS.md` / `.cursor/rules/codegraph.mdc`. Edit tool guidance here and nowhere else.
 
 ## Retrieval performance & dynamic-dispatch coverage (do not regress)
 
@@ -254,7 +253,7 @@ publish actions on shared state. Write the files, hand the user the commands.
 ## House rules
 
 - The `0.7.x` line is in active multi-agent rollout. Any change to `src/installer/` (especially `targets/`) needs corresponding test coverage and a CHANGELOG entry — installer regressions break every new install silently.
-- When changing what the MCP tools do or how agents should use them, update **all three** of `src/mcp/server-instructions.ts`, `src/installer/instructions-template.ts`, and `.cursor/rules/codegraph.mdc` — they're written to different places but say the same thing.
+- When changing what the MCP tools do or how agents should use them, edit `src/mcp/server-instructions.ts` — it is the **single source of truth** for agent-facing tool guidance (issue #529). The installer no longer writes a duplicate instructions block into `CLAUDE.md` / `AGENTS.md` / `GEMINI.md` / `.cursor/rules/codegraph.mdc` / Kiro steering, so there's nothing to keep in sync anymore. (The repo's own checked-in `.cursor/rules/codegraph.mdc` is dogfooding config — update it too if you use Cursor on this repo, but it ships nowhere.)
 - CodeGraph provides **code context**, not product requirements. For new features, ask the user about UX, edge cases, and acceptance criteria — the graph won't tell you.
 - **When the user references issues, PR comments, or external reports, anchor them to a date and version before drawing conclusions.** Check the comment's `createdAt` against:
   - The **last released version** — `grep -m1 '^## \[' CHANGELOG.md` shows the top-of-file version (older releases follow). A comment dated before the latest `## [X.Y.Z] - YYYY-MM-DD` is reacting to *released* state — work that's only on `main` or on an unmerged branch doesn't apply.