@stupidloud/codegraph 0.8.1 → 0.9.9

package/dist/installer/targets/antigravity.js

@@ -0,0 +1,308 @@
+"use strict";
+/**
+ * Google Antigravity IDE target. Antigravity is Google's VS Code-derived
+ * multi-agent IDE; the Gemini CLI is in the process of consolidating with
+ * it under a single agent platform. Antigravity reads MCP server
+ * definitions from a separate config file from the CLI.
+ *
+ * ## Config path: unified vs legacy
+ *
+ * Antigravity recently migrated to a **unified** MCP config path shared
+ * across all Antigravity tools:
+ *
+ *   - **Unified** (post-migration, current): `~/.gemini/config/mcp_config.json`
+ *     — signalled by the `~/.gemini/config/.migrated` marker file.
+ *   - **Legacy** (pre-migration): `~/.gemini/antigravity/mcp_config.json`
+ *     — what the github-mcp-server install guide still documents.
+ *
+ * We detect the marker at install time and write to the right path. On
+ * uninstall we sweep BOTH — so a user who installed on the legacy path,
+ * was then auto-migrated by Antigravity, and re-ran `codegraph install`
+ * doesn't end up with stale codegraph entries in two files.
+ *
+ * ## Entry shape: no `type: stdio` field
+ *
+ * Antigravity rejects MCP entries that carry the `type: "stdio"` field
+ * the rest of our targets use — the working entries it manages itself
+ * (e.g. `code-review-graph`) omit it, and dropping it was load-bearing
+ * to get codegraph to appear in the Customizations UI. We build the
+ * entry locally instead of routing through `getMcpServerConfig()`.
+ *
+ * ## macOS GUI app PATH resolution
+ *
+ * Antigravity is a GUI Electron app. macOS gives Dock/Finder-launched
+ * apps a stripped PATH (`/usr/bin:/bin:/usr/sbin:/sbin`) — nvm-managed
+ * tools live outside that, so a bare `codegraph` command fails to spawn
+ * even when `which codegraph` resolves in the user's shell. We resolve
+ * `codegraph` to its absolute path on macOS at install time. (Linux GUI
+ * apps inherit user PATH; Windows uses `PATH` env directly — both are
+ * fine with the bare command.)
+ *
+ * ## Shared instructions (no GEMINI.md from here)
+ *
+ * The IDE shares `~/.gemini/GEMINI.md` with Gemini CLI for instructions
+ * — written by the `./gemini.ts` target. We deliberately don't touch it
+ * here so uninstalling Antigravity without uninstalling Gemini CLI
+ * leaves CLI instructions intact. Users who install only Antigravity
+ * still get a working MCP integration; the prefer-codegraph-over-grep
+ * guidance just won't be present unless they also install the gemini
+ * target.
+ *
+ * ## Location
+ *
+ * `supportsLocation('local')` returns false — Antigravity has no
+ * project-scoped config concept as of 2026-05.
+ */
+var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    var desc = Object.getOwnPropertyDescriptor(m, k);
+    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
+      desc = { enumerable: true, get: function() { return m[k]; } };
+    }
+    Object.defineProperty(o, k2, desc);
+}) : (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    o[k2] = m[k];
+}));
+var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
+    Object.defineProperty(o, "default", { enumerable: true, value: v });
+}) : function(o, v) {
+    o["default"] = v;
+});
+var __importStar = (this && this.__importStar) || (function () {
+    var ownKeys = function(o) {
+        ownKeys = Object.getOwnPropertyNames || function (o) {
+            var ar = [];
+            for (var k in o) if (Object.prototype.hasOwnProperty.call(o, k)) ar[ar.length] = k;
+            return ar;
+        };
+        return ownKeys(o);
+    };
+    return function (mod) {
+        if (mod && mod.__esModule) return mod;
+        var result = {};
+        if (mod != null) for (var k = ownKeys(mod), i = 0; i < k.length; i++) if (k[i] !== "default") __createBinding(result, mod, k[i]);
+        __setModuleDefault(result, mod);
+        return result;
+    };
+})();
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.antigravityTarget = void 0;
+const fs = __importStar(require("fs"));
+const path = __importStar(require("path"));
+const os = __importStar(require("os"));
+const child_process_1 = require("child_process");
+const shared_1 = require("./shared");
+function unifiedConfigDir() {
+    return path.join(os.homedir(), '.gemini', 'config');
+}
+function unifiedMcpConfigPath() {
+    return path.join(unifiedConfigDir(), 'mcp_config.json');
+}
+function legacyConfigDir() {
+    return path.join(os.homedir(), '.gemini', 'antigravity');
+}
+function legacyMcpConfigPath() {
+    return path.join(legacyConfigDir(), 'mcp_config.json');
+}
+function migratedMarkerPath() {
+    return path.join(unifiedConfigDir(), '.migrated');
+}
+/**
+ * Pick the right MCP config path to write to.
+ *
+ * Prefers the unified `~/.gemini/config/mcp_config.json` when Antigravity
+ * has signalled it's migrated (`.migrated` marker present, OR the
+ * unified file already exists — Antigravity creates it on first
+ * launch post-migration). Falls back to the legacy
+ * `~/.gemini/antigravity/mcp_config.json` for users on a pre-migration
+ * Antigravity build.
+ */
+function preferredMcpConfigPath() {
+    if (fs.existsSync(migratedMarkerPath()))
+        return unifiedMcpConfigPath();
+    if (fs.existsSync(unifiedMcpConfigPath()))
+        return unifiedMcpConfigPath();
+    return legacyMcpConfigPath();
+}
+/**
+ * Resolve the on-disk path of the `codegraph` binary so a Mac GUI app
+ * launched from Dock/Finder (with a stripped PATH) can find it. Falls
+ * back to the bare `codegraph` name when:
+ *
+ *  - we're not on macOS (Linux GUI apps inherit user PATH; Windows
+ *    uses env PATH directly), OR
+ *  - the lookup fails for any reason (preserving install in restricted
+ *    environments where `which`/`command -v` aren't available).
+ *
+ * Resolution prefers `command -v` (built-in, no PATH manipulation),
+ * with `which` as a fallback. Both are read via the user's interactive
+ * shell PATH at install time — that's the right PATH for finding
+ * nvm-managed tools like ours.
+ */
+function resolveCodegraphCommand() {
+    if (process.platform !== 'darwin')
+        return 'codegraph';
+    try {
+        const resolved = (0, child_process_1.execSync)('command -v codegraph || which codegraph', {
+            encoding: 'utf-8',
+            stdio: ['ignore', 'pipe', 'ignore'],
+            shell: '/bin/bash',
+            windowsHide: true,
+        }).trim();
+        if (resolved && fs.existsSync(resolved))
+            return resolved;
+    }
+    catch {
+        /* fall through to bare name */
+    }
+    return 'codegraph';
+}
+/**
+ * Build the codegraph MCP-server entry for Antigravity. Distinct from
+ * `getMcpServerConfig()` because Antigravity (a) rejects the `type`
+ * field and (b) needs an absolute command path on macOS — see file
+ * header.
+ */
+function buildAntigravityEntry() {
+    return {
+        command: resolveCodegraphCommand(),
+        args: ['serve', '--mcp'],
+    };
+}
+class AntigravityTarget {
+    id = 'antigravity';
+    displayName = 'Antigravity IDE';
+    docsUrl = 'https://antigravity.google';
+    supportsLocation(loc) {
+        return loc === 'global';
+    }
+    detect(loc) {
+        if (loc !== 'global') {
+            return { installed: false, alreadyConfigured: false };
+        }
+        const file = preferredMcpConfigPath();
+        const config = (0, shared_1.readJsonFile)(file);
+        const alreadyConfigured = !!config.mcpServers?.codegraph;
+        // "Installed" heuristic: either the unified config dir, the legacy
+        // config dir, or one of the config files exists. Antigravity creates
+        // ~/.gemini/ on first launch even before MCP configs.
+        const installed = fs.existsSync(unifiedConfigDir()) ||
+            fs.existsSync(legacyConfigDir()) ||
+            fs.existsSync(file);
+        return { installed, alreadyConfigured, configPath: file };
+    }
+    install(loc, _opts) {
+        if (loc !== 'global') {
+            return {
+                files: [],
+                notes: ['Antigravity IDE has no project-local config — re-run with --location=global.'],
+            };
+        }
+        const files = [];
+        files.push(writeMcpEntry());
+        // If the user originally installed on the legacy path and Antigravity
+        // has since migrated, strip the stale legacy entry so they don't
+        // wind up with two competing codegraph configs.
+        const legacyCleanup = cleanupLegacyEntry();
+        if (legacyCleanup)
+            files.push(legacyCleanup);
+        return {
+            files,
+            notes: ['Restart Antigravity for MCP changes to take effect.'],
+        };
+    }
+    uninstall(loc) {
+        if (loc !== 'global')
+            return { files: [] };
+        const files = [];
+        // Remove from the preferred path.
+        const preferred = preferredMcpConfigPath();
+        files.push(removeCodegraphFromFile(preferred));
+        // Also sweep the OTHER path (legacy when preferred is unified, and
+        // vice versa) — handles the migration-half-state case where codegraph
+        // got written to one file but Antigravity now reads from the other.
+        const other = preferred === unifiedMcpConfigPath()
+            ? legacyMcpConfigPath()
+            : unifiedMcpConfigPath();
+        if (preferred !== other) {
+            const otherResult = removeCodegraphFromFile(other);
+            // Only surface the secondary file if we actually touched it —
+            // a `not-found` on a file the user never had is noise.
+            if (otherResult.action === 'removed')
+                files.push(otherResult);
+        }
+        return { files };
+    }
+    printConfig(loc) {
+        if (loc !== 'global') {
+            return '# Antigravity IDE has no project-local config — use --location=global.\n';
+        }
+        const file = preferredMcpConfigPath();
+        const snippet = JSON.stringify({ mcpServers: { codegraph: buildAntigravityEntry() } }, null, 2);
+        return `# Add to ${file}\n\n${snippet}\n`;
+    }
+    describePaths(loc) {
+        if (loc !== 'global')
+            return [];
+        return [preferredMcpConfigPath()];
+    }
+}
+function writeMcpEntry() {
+    const file = preferredMcpConfigPath();
+    const dir = path.dirname(file);
+    if (!fs.existsSync(dir))
+        fs.mkdirSync(dir, { recursive: true });
+    const existing = (0, shared_1.readJsonFile)(file);
+    const before = existing.mcpServers?.codegraph;
+    const after = buildAntigravityEntry();
+    if ((0, shared_1.jsonDeepEqual)(before, after)) {
+        return { path: file, action: 'unchanged' };
+    }
+    const action = before ? 'updated' : (fs.existsSync(file) ? 'updated' : 'created');
+    if (!existing.mcpServers)
+        existing.mcpServers = {};
+    existing.mcpServers.codegraph = after;
+    (0, shared_1.writeJsonFile)(file, existing);
+    return { path: file, action };
+}
+/**
+ * Strip the codegraph entry from the legacy `~/.gemini/antigravity/mcp_config.json`
+ * if it's present AND we're writing to the unified path. Used by install
+ * to migrate users who had codegraph configured on the legacy path
+ * before Antigravity migrated their config. Returns the file action for
+ * reporting, or `null` when there's nothing to clean up.
+ */
+function cleanupLegacyEntry() {
+    if (preferredMcpConfigPath() !== unifiedMcpConfigPath())
+        return null;
+    const legacy = legacyMcpConfigPath();
+    if (!fs.existsSync(legacy))
+        return null;
+    const config = (0, shared_1.readJsonFile)(legacy);
+    if (!config.mcpServers?.codegraph)
+        return null;
+    delete config.mcpServers.codegraph;
+    if (Object.keys(config.mcpServers).length === 0) {
+        delete config.mcpServers;
+    }
+    (0, shared_1.writeJsonFile)(legacy, config);
+    return { path: legacy, action: 'removed' };
+}
+function removeCodegraphFromFile(file) {
+    if (!fs.existsSync(file))
+        return { path: file, action: 'not-found' };
+    const config = (0, shared_1.readJsonFile)(file);
+    if (!config.mcpServers?.codegraph)
+        return { path: file, action: 'not-found' };
+    delete config.mcpServers.codegraph;
+    if (Object.keys(config.mcpServers).length === 0) {
+        delete config.mcpServers;
+    }
+    // Leave a now-empty `{}` in place — Antigravity manages this file and
+    // a stray empty file is less surprising than a deletion.
+    (0, shared_1.writeJsonFile)(file, config);
+    return { path: file, action: 'removed' };
+}
+exports.antigravityTarget = new AntigravityTarget();
+//# sourceMappingURL=antigravity.js.map

package/dist/installer/targets/antigravity.js.map

@@ -0,0 +1 @@
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package/dist/installer/targets/claude.d.ts

@@ -25,7 +25,32 @@ import { AgentTarget, Location, WriteResult } from './types';
  * cause side effects callers don't expect.
  */
 export declare function writeMcpEntry(loc: Location): WriteResult['files'][number];
+/**
+ * Remove stale codegraph auto-sync hooks from Claude `settings.json`.
+ *
+ * Surgical at the individual-command level: only entries matching
+ * `isLegacyCodegraphHookCommand` are dropped, so a sibling hook sharing
+ * a matcher group (or the Stop event) with ours survives. We prune a
+ * matcher group only once its `hooks` array is empty, an event only
+ * once it has no groups left, and `hooks` itself only once every event
+ * is gone — and none of that runs unless we actually removed a
+ * codegraph command, so a settings.json with no legacy hooks is left
+ * byte-for-byte untouched and reported `unchanged`.
+ *
+ * Exported so it can be unit-tested directly and reused by both
+ * `install` (an upgrade self-heals) and `uninstall`.
+ */
+export declare function cleanupLegacyHooks(loc: Location): WriteResult['files'][number];
 export declare function writePermissionsEntry(loc: Location): WriteResult['files'][number];
-export declare function writeInstructionsEntry(loc: Location): WriteResult['files'][number];
+/**
+ * Strip the marker-delimited CodeGraph block from CLAUDE.md if a prior
+ * install wrote one. Codegraph no longer maintains an instructions file
+ * (issue #529) — the MCP server's `initialize` instructions are the
+ * single source of truth — so both install (self-heal on upgrade) and
+ * uninstall call this. `removeMarkedSection` returns `not-found`/`kept`
+ * when there's nothing to strip; the install caller drops those from
+ * the report so a fresh install stays quiet.
+ */
+export declare function removeInstructionsEntry(loc: Location): WriteResult['files'][number];
 export declare const claudeTarget: AgentTarget;
 //# sourceMappingURL=claude.d.ts.map

package/dist/installer/targets/claude.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"claude.d.ts","sourceRoot":"","sources":["../../../src/installer/targets/claude.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;GAiBG;AAKH,OAAO,EACL,WAAW,EAGX,QAAQ,EACR,WAAW,EACZ,MAAM,SAAS,CAAC;AAiKjB;;;;;;GAMG;AACH,wBAAgB,aAAa,CAAC,GAAG,EAAE,QAAQ,GAAG,WAAW,CAAC,OAAO,CAAC,CAAC,MAAM,CAAC,CAsBzE;AAyBD,wBAAgB,qBAAqB,CAAC,GAAG,EAAE,QAAQ,GAAG,WAAW,CAAC,OAAO,CAAC,CAAC,MAAM,CAAC,CAoBjF;AAED,wBAAgB,sBAAsB,CAAC,GAAG,EAAE,QAAQ,GAAG,WAAW,CAAC,OAAO,CAAC,CAAC,MAAM,CAAC,CA0ClF;AAED,eAAO,MAAM,YAAY,EAAE,WAAoC,CAAC"}
+{"version":3,"file":"claude.d.ts","sourceRoot":"","sources":["../../../src/installer/targets/claude.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;GAiBG;AAKH,OAAO,EACL,WAAW,EAGX,QAAQ,EACR,WAAW,EACZ,MAAM,SAAS,CAAC;AAoLjB;;;;;;GAMG;AACH,wBAAgB,aAAa,CAAC,GAAG,EAAE,QAAQ,GAAG,WAAW,CAAC,OAAO,CAAC,CAAC,MAAM,CAAC,CAsBzE;AA6CD;;;;;;;;;;;;;;GAcG;AACH,wBAAgB,kBAAkB,CAAC,GAAG,EAAE,QAAQ,GAAG,WAAW,CAAC,OAAO,CAAC,CAAC,MAAM,CAAC,CA0C9E;AAED,wBAAgB,qBAAqB,CAAC,GAAG,EAAE,QAAQ,GAAG,WAAW,CAAC,OAAO,CAAC,CAAC,MAAM,CAAC,CAoBjF;AAED;;;;;;;;GAQG;AACH,wBAAgB,uBAAuB,CAAC,GAAG,EAAE,QAAQ,GAAG,WAAW,CAAC,OAAO,CAAC,CAAC,MAAM,CAAC,CAInF;AAED,eAAO,MAAM,YAAY,EAAE,WAAoC,CAAC"}

package/dist/installer/targets/claude.js

@@ -53,8 +53,9 @@ var __importStar = (this && this.__importStar) || (function () {
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.claudeTarget = void 0;
 exports.writeMcpEntry = writeMcpEntry;
+exports.cleanupLegacyHooks = cleanupLegacyHooks;
 exports.writePermissionsEntry = writePermissionsEntry;
-exports.writeInstructionsEntry = writeInstructionsEntry;
+exports.removeInstructionsEntry = removeInstructionsEntry;
 const fs = __importStar(require("fs"));
 const path = __importStar(require("path"));
 const os = __importStar(require("os"));
@@ -124,8 +125,25 @@ class ClaudeCodeTarget {
         if (opts.autoAllow) {
             files.push(writePermissionsEntry(loc));
         }
-        // 3. CLAUDE.md instructions
-        files.push(writeInstructionsEntry(loc));
+        // 2b. Strip stale auto-sync hooks left by a pre-0.8 install. Those
+        // versions wrote `codegraph mark-dirty` / `sync-if-dirty` hooks to
+        // settings.json; both subcommands are gone from the CLI, so the
+        // Stop hook now fails every turn with "unknown command
+        // 'sync-if-dirty'". Cleaning up on install makes an upgrade
+        // self-healing. Only surfaced when something was actually removed.
+        const hookCleanup = cleanupLegacyHooks(loc);
+        if (hookCleanup.action === 'removed')
+            files.push(hookCleanup);
+        // 3. CLAUDE.md instructions — no longer written. The codegraph
+        // usage guidance now ships solely in the MCP server's `initialize`
+        // response (see `mcp/server-instructions.ts`), which Claude Code
+        // surfaces in the system prompt automatically. Writing it into
+        // CLAUDE.md as well meant the agent read the same playbook twice
+        // every turn (issue #529). Strip any block a previous install left
+        // behind so an upgrade self-heals — same idiom as the hook cleanup.
+        const instrCleanup = removeInstructionsEntry(loc);
+        if (instrCleanup.action === 'removed')
+            files.push(instrCleanup);
         return { files };
     }
     uninstall(loc) {
@@ -174,10 +192,16 @@ class ClaudeCodeTarget {
         else {
             files.push({ path: settingsPath, action: 'not-found' });
         }
-        // 3. Instructions
-        const instr = instructionsPath(loc);
-        const action = (0, shared_1.removeMarkedSection)(instr, instructions_template_1.CODEGRAPH_SECTION_START, instructions_template_1.CODEGRAPH_SECTION_END);
-        files.push({ path: instr, action });
+        // 2b. Strip any stale auto-sync hooks a pre-0.8 install left in
+        // settings.json. The hook-cleanup step was lost when the installer
+        // moved to the per-target architecture; restoring it here means
+        // uninstall — and the npm `preuninstall` hook that drives it — fully
+        // reverses a legacy install.
+        const hookCleanup = cleanupLegacyHooks(loc);
+        if (hookCleanup.action === 'removed')
+            files.push(hookCleanup);
+        // 3. Instructions — strip the legacy CodeGraph block if present.
+        files.push(removeInstructionsEntry(loc));
         return { files };
     }
     printConfig(loc) {
@@ -248,6 +272,81 @@ function cleanupLegacyLocalMcp() {
     }
     return { path: file, action: 'removed' };
 }
+/**
+ * True when a Claude Code hook `command` is one of the auto-sync hooks
+ * a pre-0.8 install wrote. Those installers added
+ * `PostToolUse(Edit|Write) → codegraph mark-dirty` and
+ * `Stop → codegraph sync-if-dirty` (local builds used the
+ * `npx @colbymchenry/codegraph …` form, which still contains the
+ * `codegraph <subcommand>` substring). Both subcommands were later
+ * removed from the CLI, so the Stop hook fails every turn with
+ * "unknown command 'sync-if-dirty'". Matching on the codegraph-scoped
+ * subcommand keeps unrelated user hooks (e.g. GitKraken's
+ * `gk ai hook run`) untouched.
+ */
+function isLegacyCodegraphHookCommand(command) {
+    if (typeof command !== 'string')
+        return false;
+    return (command.includes('codegraph mark-dirty') ||
+        command.includes('codegraph sync-if-dirty'));
+}
+/**
+ * Remove stale codegraph auto-sync hooks from Claude `settings.json`.
+ *
+ * Surgical at the individual-command level: only entries matching
+ * `isLegacyCodegraphHookCommand` are dropped, so a sibling hook sharing
+ * a matcher group (or the Stop event) with ours survives. We prune a
+ * matcher group only once its `hooks` array is empty, an event only
+ * once it has no groups left, and `hooks` itself only once every event
+ * is gone — and none of that runs unless we actually removed a
+ * codegraph command, so a settings.json with no legacy hooks is left
+ * byte-for-byte untouched and reported `unchanged`.
+ *
+ * Exported so it can be unit-tested directly and reused by both
+ * `install` (an upgrade self-heals) and `uninstall`.
+ */
+function cleanupLegacyHooks(loc) {
+    const file = settingsJsonPath(loc);
+    if (!fs.existsSync(file))
+        return { path: file, action: 'not-found' };
+    const settings = (0, shared_1.readJsonFile)(file);
+    const hooks = settings.hooks;
+    if (!hooks || typeof hooks !== 'object' || Array.isArray(hooks)) {
+        return { path: file, action: 'unchanged' };
+    }
+    // Pass 1: drop the legacy command(s) from inside every matcher group.
+    let removedAny = false;
+    for (const event of Object.keys(hooks)) {
+        const groups = hooks[event];
+        if (!Array.isArray(groups))
+            continue;
+        for (const group of groups) {
+            if (!group || !Array.isArray(group.hooks))
+                continue;
+            const before = group.hooks.length;
+            group.hooks = group.hooks.filter((h) => !isLegacyCodegraphHookCommand(h?.command));
+            if (group.hooks.length !== before)
+                removedAny = true;
+        }
+    }
+    if (!removedAny)
+        return { path: file, action: 'unchanged' };
+    // Pass 2: prune empty matcher groups, then events with no groups
+    // left, then an empty top-level `hooks`. Guarded by `removedAny` so
+    // we never restructure a settings.json that had no codegraph hooks.
+    for (const event of Object.keys(hooks)) {
+        const groups = hooks[event];
+        if (!Array.isArray(groups))
+            continue;
+        hooks[event] = groups.filter((g) => !(g && Array.isArray(g.hooks) && g.hooks.length === 0));
+        if (hooks[event].length === 0)
+            delete hooks[event];
+    }
+    if (Object.keys(hooks).length === 0)
+        delete settings.hooks;
+    (0, shared_1.writeJsonFile)(file, settings);
+    return { path: file, action: 'removed' };
+}
 function writePermissionsEntry(loc) {
     const file = settingsJsonPath(loc);
     const settings = (0, shared_1.readJsonFile)(file);
@@ -269,40 +368,19 @@ function writePermissionsEntry(loc) {
     (0, shared_1.writeJsonFile)(file, settings);
     return { path: file, action: created ? 'created' : 'updated' };
 }
-function writeInstructionsEntry(loc) {
+/**
+ * Strip the marker-delimited CodeGraph block from CLAUDE.md if a prior
+ * install wrote one. Codegraph no longer maintains an instructions file
+ * (issue #529) — the MCP server's `initialize` instructions are the
+ * single source of truth — so both install (self-heal on upgrade) and
+ * uninstall call this. `removeMarkedSection` returns `not-found`/`kept`
+ * when there's nothing to strip; the install caller drops those from
+ * the report so a fresh install stays quiet.
+ */
+function removeInstructionsEntry(loc) {
     const file = instructionsPath(loc);
-    // Ensure config dir exists (for global ~/.claude/).
-    const dir = path.dirname(file);
-    if (!fs.existsSync(dir))
-        fs.mkdirSync(dir, { recursive: true });
-    // Honor the legacy "unmarked ## CodeGraph" rewrite path that the
-    // original installer supported (some users hand-pasted a section
-    // before markers existed). Detect first and migrate inline.
-    if (fs.existsSync(file)) {
-        const content = fs.readFileSync(file, 'utf-8');
-        if (!content.includes(instructions_template_1.CODEGRAPH_SECTION_START)) {
-            const headerMatch = content.match(/\n## CodeGraph\n/);
-            if (headerMatch && headerMatch.index !== undefined) {
-                const sectionStart = headerMatch.index;
-                const after = content.substring(sectionStart + 1);
-                const nextHeader = after.match(/\n## (?!#)/);
-                const sectionEnd = nextHeader && nextHeader.index !== undefined
-                    ? sectionStart + 1 + nextHeader.index
-                    : content.length;
-                const merged = content.substring(0, sectionStart) +
-                    '\n' + instructions_template_1.INSTRUCTIONS_TEMPLATE +
-                    content.substring(sectionEnd);
-                (0, shared_1.atomicWriteFileSync)(file, merged);
-                return { path: file, action: 'updated' };
-            }
-        }
-    }
-    const action = (0, shared_1.replaceOrAppendMarkedSection)(file, instructions_template_1.INSTRUCTIONS_TEMPLATE, instructions_template_1.CODEGRAPH_SECTION_START, instructions_template_1.CODEGRAPH_SECTION_END);
-    // Map the four-state action to WriteResult's action vocabulary.
-    const mapped = action === 'created' ? 'created'
-        : action === 'unchanged' ? 'unchanged'
-            : 'updated';
-    return { path: file, action: mapped };
+    const action = (0, shared_1.removeMarkedSection)(file, instructions_template_1.CODEGRAPH_SECTION_START, instructions_template_1.CODEGRAPH_SECTION_END);
+    return { path: file, action };
 }
 exports.claudeTarget = new ClaudeCodeTarget();
 //# sourceMappingURL=claude.js.map

package/dist/installer/targets/claude.js.map

@@ -1 +1 @@
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package/dist/installer/targets/codex.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"codex.d.ts","sourceRoot":"","sources":["../../../src/installer/targets/codex.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;GAcG;AAKH,OAAO,EACL,WAAW,EAKZ,MAAM,SAAS,CAAC;AA2JjB,eAAO,MAAM,WAAW,EAAE,WAA+B,CAAC"}
+{"version":3,"file":"codex.d.ts","sourceRoot":"","sources":["../../../src/installer/targets/codex.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;GAcG;AAKH,OAAO,EACL,WAAW,EAKZ,MAAM,SAAS,CAAC;AAqJjB,eAAO,MAAM,WAAW,EAAE,WAA+B,CAAC"}

package/dist/installer/targets/codex.js

@@ -97,7 +97,12 @@ class CodexTarget {
         }
         const files = [];
         files.push(writeMcpEntry());
-        files.push(writeInstructionsEntry());
+        // AGENTS.md is no longer written — the codegraph usage guidance
+        // ships in the MCP server's `initialize` response (issue #529).
+        // Strip a block a previous install left so an upgrade self-heals.
+        const instrCleanup = removeInstructionsEntry();
+        if (instrCleanup.action === 'removed')
+            files.push(instrCleanup);
         return { files };
     }
     uninstall(loc) {
@@ -127,9 +132,7 @@ class CodexTarget {
         else {
             files.push({ path: tomlPath, action: 'not-found' });
         }
-        const instr = instructionsPath();
-        const instrAction = (0, shared_1.removeMarkedSection)(instr, instructions_template_1.CODEGRAPH_SECTION_START, instructions_template_1.CODEGRAPH_SECTION_END);
-        files.push({ path: instr, action: instrAction });
+        files.push(removeInstructionsEntry());
         return { files };
     }
     printConfig(loc) {
@@ -170,16 +173,15 @@ function writeMcpEntry() {
     (0, shared_1.atomicWriteFileSync)(file, nextContent);
     return { path: file, action: created ? 'created' : 'updated' };
 }
-function writeInstructionsEntry() {
+/**
+ * Strip the marker-delimited CodeGraph block from `~/.codex/AGENTS.md`
+ * if a prior install wrote one. Used by both install (self-heal on
+ * upgrade) and uninstall — see issue #529.
+ */
+function removeInstructionsEntry() {
     const file = instructionsPath();
-    const dir = path.dirname(file);
-    if (!fs.existsSync(dir))
-        fs.mkdirSync(dir, { recursive: true });
-    const action = (0, shared_1.replaceOrAppendMarkedSection)(file, instructions_template_1.INSTRUCTIONS_TEMPLATE, instructions_template_1.CODEGRAPH_SECTION_START, instructions_template_1.CODEGRAPH_SECTION_END);
-    const mapped = action === 'created' ? 'created'
-        : action === 'unchanged' ? 'unchanged'
-            : 'updated';
-    return { path: file, action: mapped };
+    const action = (0, shared_1.removeMarkedSection)(file, instructions_template_1.CODEGRAPH_SECTION_START, instructions_template_1.CODEGRAPH_SECTION_END);
+    return { path: file, action };
 }
 exports.codexTarget = new CodexTarget();
 //# sourceMappingURL=codex.js.map