codesift-mcp 0.15.5 → 0.19.2

package/dist/cli/owner-only-file.js.map

@@ -1 +1 @@
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package/dist/cli/service.d.ts

@@ -89,6 +89,38 @@ export declare function buildServicePlan(opts: {
  * killing the process alone just makes launchd start it again, which is the
  * whole point.
  */
+/**
+ * Heap ceiling for the daemon, in MB.
+ *
+ * The daemon ran with V8's DEFAULT limit, which is derived from the machine but
+ * tops out around 4 GB — on a 128 GB box it was 4288 MB. That is not enough for
+ * what this process actually is: one long-lived server for every project on the
+ * machine, materialising whole indexes (a 240k-symbol index is ~349 MB resident)
+ * and holding two RAM-scaled caches on top. It reached 4.69 GB and died with
+ * `FatalProcessOutOfMemory`, launchd restarted it, and it did it again — 14 node
+ * crash reports in 24 h on 2026-08-28.
+ *
+ * The crash loop is the damaging part, not the single crash: an OOM discards ALL
+ * in-flight work, so a mass re-index (29 repos rebuilding hash snapshots) never
+ * reaches the end, and the next process starts the same work over. Raising the
+ * ceiling is what lets that pass finish once.
+ *
+ * Scaled, not fixed, and CAPPED: a ceiling is also the only thing standing
+ * between a genuine leak and the whole machine, so it stays well below total RAM.
+ * The cap was 8192 for one afternoon and that was too conservative — a 128 GB
+ * workstation running dozens of agents got the same ceiling as a 64 GB one, while
+ * the crash it had to prevent happened at 4.7 GB. RAM/8 with a 24 GB cap gives
+ * this machine 16 GB: comfortably past the observed peak, still an eighth of the
+ * box, and still a bound rather than a blank cheque.
+ * `CODESIFT_DAEMON_HEAP_MB` overrides for a machine that needs something else.
+ *
+ * NOTE this is a ceiling, not a diagnosis. It does not prove the growth is
+ * legitimate; it buys the room the observed workload needs and turns a crash loop
+ * into a slow pass. If the daemon starts reaching THIS limit too, the answer is
+ * the ADR-004 stage-2 work (query the DB instead of materialising indexes), not a
+ * bigger number here.
+ */
+export declare function resolveDaemonHeapMb(totalRamBytes: number, env?: NodeJS.ProcessEnv): number;
 export declare function buildLaunchAgentPlist(plan: ServicePlan): string;
 /**
  * One `Environment=` assignment, quoted so the VALUE cannot become unit syntax.

package/dist/cli/service.d.ts.map

@@ -1 +1 @@
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package/dist/cli/service.js

@@ -1,5 +1,5 @@
 import { mkdirSync, readFileSync, existsSync, unlinkSync } from "node:fs";
-import { homedir, platform } from "node:os";
+import { homedir, platform, totalmem } from "node:os";
 import { join, dirname } from "node:path";
 import { isLoopbackHost } from "../utils/loopback.js";
 import { writeOwnerOnlyFileSync } from "./owner-only-file.js";
@@ -99,8 +99,70 @@ export function buildServicePlan(opts) {
  * killing the process alone just makes launchd start it again, which is the
  * whole point.
  */
+/**
+ * Heap ceiling for the daemon, in MB.
+ *
+ * The daemon ran with V8's DEFAULT limit, which is derived from the machine but
+ * tops out around 4 GB — on a 128 GB box it was 4288 MB. That is not enough for
+ * what this process actually is: one long-lived server for every project on the
+ * machine, materialising whole indexes (a 240k-symbol index is ~349 MB resident)
+ * and holding two RAM-scaled caches on top. It reached 4.69 GB and died with
+ * `FatalProcessOutOfMemory`, launchd restarted it, and it did it again — 14 node
+ * crash reports in 24 h on 2026-08-28.
+ *
+ * The crash loop is the damaging part, not the single crash: an OOM discards ALL
+ * in-flight work, so a mass re-index (29 repos rebuilding hash snapshots) never
+ * reaches the end, and the next process starts the same work over. Raising the
+ * ceiling is what lets that pass finish once.
+ *
+ * Scaled, not fixed, and CAPPED: a ceiling is also the only thing standing
+ * between a genuine leak and the whole machine, so it stays well below total RAM.
+ * The cap was 8192 for one afternoon and that was too conservative — a 128 GB
+ * workstation running dozens of agents got the same ceiling as a 64 GB one, while
+ * the crash it had to prevent happened at 4.7 GB. RAM/8 with a 24 GB cap gives
+ * this machine 16 GB: comfortably past the observed peak, still an eighth of the
+ * box, and still a bound rather than a blank cheque.
+ * `CODESIFT_DAEMON_HEAP_MB` overrides for a machine that needs something else.
+ *
+ * NOTE this is a ceiling, not a diagnosis. It does not prove the growth is
+ * legitimate; it buys the room the observed workload needs and turns a crash loop
+ * into a slow pass. If the daemon starts reaching THIS limit too, the answer is
+ * the ADR-004 stage-2 work (query the DB instead of materialising indexes), not a
+ * bigger number here.
+ */
+export function resolveDaemonHeapMb(totalRamBytes, env = process.env) {
+    const override = Number(env["CODESIFT_DAEMON_HEAP_MB"]);
+    if (Number.isFinite(override) && override >= 512)
+        return Math.floor(override);
+    const ramMb = totalRamBytes / (1024 * 1024);
+    return Math.min(24576, Math.max(2048, Math.floor(ramMb / 8)));
+}
 export function buildLaunchAgentPlist(plan) {
-    const args = [plan.cliPath, "serve", "--port", String(plan.port), "--host", plan.host];
+    // Node options must precede the script path, or node treats them as script args
+    // and they are silently ignored — the failure mode being an unchanged limit and
+    // a plist that looks correct.
+    const heapMb = resolveDaemonHeapMb(totalmem());
+    const args = [
+        `--max-old-space-size=${heapMb}`,
+        // Young generation, left at V8's default until 2026-08-28 — which for a large heap is ~16 MB,
+        // so scavenges fire constantly. Each one walks every old-generation memory chunk, and this
+        // daemon deliberately keeps a LARGE old generation (4 GB of index cache) so repos stay resident.
+        // Sampled under load: 35% of main-thread time in Heap::CollectGarbage, 33% of it inside
+        // OldGenerationMemoryChunkIterator::next — and each pause stalls the event loop, so /health
+        // answered in 2 s, then 3.5 s, then not at all, and clients read that as a dead server.
+        //
+        // A bigger semi-space means FEWER scavenges (each slightly longer), which is the trade that
+        // fits a process whose old generation is large by design. This is the other half of the cache
+        // budget increase: without it, that change bought fast reads and paid in GC pauses.
+        "--max-semi-space-size=64",
+        plan.cliPath, "serve", "--port", String(plan.port), "--host", plan.host,
+    ];
+    // ProcessType is Standard, not Background. Background puts the process in the macOS background
+    // band (scheduler priority 4 against 31 for an ordinary process), which is invisible on an idle
+    // machine and fatal on a busy one: every agent session blocks on this daemon, and under load
+    // 100-160 a priority-4 process barely runs. Sampled 2026-09-24: a freshly restarted daemon sat
+    // 6+ minutes at 0% CPU still inside Node's own bootstrap (compiling builtins) — it had not
+    // executed a line of CodeSift yet — while every client reported "codesift unavailable".
     const argLines = [plan.execPath, ...args]
         .map((a) => `    <string>${escapeXml(a)}</string>`)
         .join("\n");
@@ -121,7 +183,7 @@ ${argLines}
   <key>ThrottleInterval</key>
   <integer>10</integer>
   <key>ProcessType</key>
-  <string>Background</string>
+  <string>Standard</string>
   <key>EnvironmentVariables</key>
   <dict>
     <key>PATH</key>
@@ -159,7 +221,15 @@ export function systemdEnv(key, value) {
 }
 /** Linux systemd *user* unit — same supervision contract as the LaunchAgent. */
 export function buildSystemdUnit(plan) {
-    const exec = [plan.execPath, plan.cliPath, "serve", "--port", String(plan.port), "--host", plan.host]
+    // Same heap ceiling as the LaunchAgent, and for the same reason — see
+    // resolveDaemonHeapMb. A Linux host runs the identical workload, so leaving it
+    // on V8's default here would just move the crash loop to the other platform.
+    const exec = [
+        plan.execPath,
+        `--max-old-space-size=${resolveDaemonHeapMb(totalmem())}`,
+        "--max-semi-space-size=64",
+        plan.cliPath, "serve", "--port", String(plan.port), "--host", plan.host,
+    ]
         .map((a) => (/[\s"']/.test(a) ? JSON.stringify(a) : a))
         .join(" ");
     return `[Unit]

package/dist/cli/service.js.map

@@ -1 +1 @@
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package/dist/cli/setup/claude.js

@@ -2,7 +2,7 @@ import { existsSync } from "node:fs";
 import { homedir } from "node:os";
 import { join } from "node:path";
 import { ensureDir, readJsonFile, writeJsonFile } from "./fs.js";
-import { ensureHookEntry, hasCodesiftHook, loadHooksSection } from "./hooks.js";
+import { ensureHookEntry, hasCodesiftHook, loadHooksSection, saveHooksSection } from "./hooks.js";
 import { setupJsonPlatform } from "./mcp.js";
 const CLAUDE_CONFIG = { configDirName: ".claude", configFileName: "settings.json" };
 const STDIN_HOOK_SUBCOMMANDS = [
@@ -109,7 +109,7 @@ export async function setupClaudeHooks() {
     const configDir = join(homedir(), ".claude");
     const settingsPath = join(configDir, "settings.json");
     await ensureDir(configDir);
-    const { root, hooks } = await loadHooksSection(settingsPath);
+    const { root, hooks, original } = await loadHooksSection(settingsPath);
     for (const [event, entries] of Object.entries(CLAUDE_HOOKS)) {
         for (const entry of entries) {
             ensureHookEntry(hooks, event, entry);
@@ -117,7 +117,7 @@ export async function setupClaudeHooks() {
     }
     upgradeStdinHookCommands(hooks);
     removeRetiredClaudeHooks(hooks);
-    await writeJsonFile(settingsPath, root);
+    await saveHooksSection(settingsPath, root, original);
     await migrateLegacyClaudeHooks(configDir);
 }
 //# sourceMappingURL=claude.js.map

package/dist/cli/setup/claude.js.map

@@ -1 +1 @@
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package/dist/cli/setup/codex-project-auto.d.ts

@@ -0,0 +1,27 @@
+/**
+ * Give a repository its own Codex config so the daemon knows where the session works.
+ *
+ * Codex keeps MCP configuration in ONE global file, and an HTTP entry carries exactly one
+ * directory — so the global entry is deliberately bare (`/mcp`, no `?cwd=`). Without a
+ * per-project file the daemon therefore has no working directory at all and answers
+ * "does not know your working directory"; repo auto-resolution, which is the documented
+ * default, fails for every tool. Measured 2026-08-29: 31 working trees on this machine,
+ * ZERO with a project config, and a Codex session in one of them concluded CodeSift could
+ * not see its files.
+ *
+ * Doing it at registration rather than by hand is the point: a repository that CodeSift has
+ * just indexed is exactly a repository a Codex session is about to ask about.
+ */
+export type CodexProjectConfigOutcome = "written" | "already-present" | "upgraded" | "skipped-linked-worktree" | "skipped-codex-not-http" | "skipped-no-codex" | "skipped-disabled" | "failed";
+/**
+ * Write `<root>/.codex/config.toml` when — and only when — it is safe and useful.
+ *
+ * Best effort by design: this runs inside repository registration, and a repository must
+ * register whether or not a client's config could be written. Every outcome is a value, not a
+ * throw.
+ */
+export declare function ensureCodexProjectConfig(root: string, options?: {
+    env?: NodeJS.ProcessEnv;
+    home?: string;
+}): Promise<CodexProjectConfigOutcome>;
+//# sourceMappingURL=codex-project-auto.d.ts.map

package/dist/cli/setup/codex-project-auto.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"codex-project-auto.d.ts","sourceRoot":"","sources":["../../../src/cli/setup/codex-project-auto.ts"],"names":[],"mappings":"AAQA;;;;;;;;;;;;;GAaG;AACH,MAAM,MAAM,yBAAyB,GACjC,SAAS,GACT,iBAAiB,GACjB,UAAU,GACV,yBAAyB,GACzB,wBAAwB,GACxB,kBAAkB,GAClB,kBAAkB,GAClB,QAAQ,CAAC;AAkCb;;;;;;GAMG;AACH,wBAAsB,wBAAwB,CAC5C,IAAI,EAAE,MAAM,EACZ,OAAO,CAAC,EAAE;IAAE,GAAG,CAAC,EAAE,MAAM,CAAC,UAAU,CAAC;IAAC,IAAI,CAAC,EAAE,MAAM,CAAA;CAAE,GACnD,OAAO,CAAC,yBAAyB,CAAC,CA0CpC"}

package/dist/cli/setup/codex-project-auto.js

@@ -0,0 +1,98 @@
+import { existsSync } from "node:fs";
+import { readFile } from "node:fs/promises";
+import { homedir } from "node:os";
+import { join } from "node:path";
+import { findWorkingTree } from "../../utils/worktree.js";
+import { setupCodex } from "./codex.js";
+/** Opt out with CODESIFT_CODEX_PROJECT_CONFIG=0. */
+function disabled(env) {
+    const raw = env["CODESIFT_CODEX_PROJECT_CONFIG"];
+    return raw === "0" || raw === "false";
+}
+/**
+ * Is the GLOBAL Codex entry an HTTP one?
+ *
+ * This gate is not politeness, it is correctness. Codex MERGES a project file into the global
+ * one per key, and a project `url` on top of a global `command` produces a hybrid it refuses to
+ * load at all: `Error loading config.toml: url is not supported for stdio`. That failure takes
+ * down EVERY other MCP server in the file, not just codesift — so writing a project config
+ * against a stdio global is far worse than writing nothing.
+ */
+async function globalCodexEntryIsHttp(home) {
+    const globalToml = join(home, ".codex", "config.toml");
+    if (!existsSync(globalToml))
+        return false;
+    let content;
+    try {
+        content = await readFile(globalToml, "utf-8");
+    }
+    catch {
+        return false;
+    }
+    const marker = content.indexOf("[mcp_servers.codesift]");
+    if (marker < 0)
+        return false;
+    const rest = content.slice(marker + "[mcp_servers.codesift]".length);
+    const nextSection = rest.search(/^\s*\[/m);
+    const block = nextSection >= 0 ? rest.slice(0, nextSection) : rest;
+    return /^\s*url\s*=/m.test(block);
+}
+/**
+ * Write `<root>/.codex/config.toml` when — and only when — it is safe and useful.
+ *
+ * Best effort by design: this runs inside repository registration, and a repository must
+ * register whether or not a client's config could be written. Every outcome is a value, not a
+ * throw.
+ */
+export async function ensureCodexProjectConfig(root, options) {
+    const env = options?.env ?? process.env;
+    const home = options?.home ?? homedir();
+    if (disabled(env))
+        return "skipped-disabled";
+    // LINKED WORKTREES ARE DELIBERATELY EXCLUDED. Pointing a worktree at itself makes the daemon
+    // index it as a repository of its own, and 27 of those starting at once is what saturated this
+    // machine for hours on 2026-08-28. Main checkouts only; a worktree stays on its parent's index
+    // until someone opts it in by hand.
+    const tree = findWorkingTree(root);
+    if (!tree || tree.linked)
+        return "skipped-linked-worktree";
+    // An existing file is left alone — someone wrote it on purpose — EXCEPT when it predates
+    // per-client tool lists. Codex merges the project file into the global one per key, so a project
+    // `url` without `client=` OVERRIDES the global one that has it, and this project silently loses
+    // the front-loaded surface the global entry was fixed to provide.
+    const projectToml = join(root, ".codex", "config.toml");
+    if (existsSync(projectToml)) {
+        let existing = "";
+        try {
+            existing = await readFile(projectToml, "utf-8");
+        }
+        catch {
+            return "already-present";
+        }
+        if (!/^\s*url\s*=\s*"[^"]*[?&]client=/m.test(existing)) {
+            try {
+                await setupCodex({ http: true, projectScope: true, cwd: root, hooks: false, rules: false });
+                return "upgraded";
+            }
+            catch {
+                return "failed";
+            }
+        }
+        return "already-present";
+    }
+    if (!existsSync(join(home, ".codex")))
+        return "skipped-no-codex";
+    if (!(await globalCodexEntryIsHttp(home)))
+        return "skipped-codex-not-http";
+    try {
+        // `cwd` is BOTH the directory pinned into the URL and the directory the project file is
+        // written into — setupCodex derives projectRoot from it. Hooks and rules stay off: this is
+        // about one client entry, not about reconfiguring someone's repository.
+        await setupCodex({ http: true, projectScope: true, cwd: tree.root, hooks: false, rules: false });
+        return "written";
+    }
+    catch {
+        return "failed";
+    }
+}
+//# sourceMappingURL=codex-project-auto.js.map

package/dist/cli/setup/codex-project-auto.js.map

@@ -0,0 +1 @@
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package/dist/cli/setup/codex.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"codex.d.ts","sourceRoot":"","sources":["../../../src/cli/setup/codex.ts"],"names":[],"mappings":"AAIA,OAAO,KAAK,EAAE,YAAY,EAAE,WAAW,EAAE,MAAM,YAAY,CAAC;AAK5D,wBAAgB,kCAAkC,CAChD,OAAO,EAAE,MAAM,GACd;IAAE,OAAO,EAAE,MAAM,CAAC;IAAC,OAAO,EAAE,MAAM,CAAA;CAAE,CAUtC;AAED,wBAAgB,yCAAyC,CACvD,OAAO,EAAE,MAAM,GACd;IAAE,OAAO,EAAE,MAAM,CAAC;IAAC,OAAO,EAAE,OAAO,CAAA;CAAE,CA8BvC;AA4HD,wBAAsB,UAAU,CAAC,OAAO,CAAC,EAAE,YAAY,GAAG,OAAO,CAAC,WAAW,CAAC,CA+B7E;AAED,wBAAsB,eAAe,IAAI,OAAO,CAAC,IAAI,CAAC,CAerD"}
+{"version":3,"file":"codex.d.ts","sourceRoot":"","sources":["../../../src/cli/setup/codex.ts"],"names":[],"mappings":"AAIA,OAAO,KAAK,EAAE,YAAY,EAAE,WAAW,EAAE,MAAM,YAAY,CAAC;AAK5D,wBAAgB,kCAAkC,CAChD,OAAO,EAAE,MAAM,GACd;IAAE,OAAO,EAAE,MAAM,CAAC;IAAC,OAAO,EAAE,MAAM,CAAA;CAAE,CAUtC;AAED,wBAAgB,yCAAyC,CACvD,OAAO,EAAE,MAAM,GACd;IAAE,OAAO,EAAE,MAAM,CAAC;IAAC,OAAO,EAAE,OAAO,CAAA;CAAE,CA8BvC;AA4LD,wBAAsB,UAAU,CAAC,OAAO,CAAC,EAAE,YAAY,GAAG,OAAO,CAAC,WAAW,CAAC,CAmE7E;AAED,wBAAsB,eAAe,IAAI,OAAO,CAAC,IAAI,CAAC,CAerD"}

package/dist/cli/setup/codex.js

@@ -1,10 +1,10 @@
 import { existsSync } from "node:fs";
-import { readFile } from "node:fs/promises";
+import { readFile, writeFile } from "node:fs/promises";
 import { homedir } from "node:os";
 import { join } from "node:path";
-import { ensureDir, writeJsonFile, writeSecretFile } from "./fs.js";
+import { ensureDir, writeSecretFile } from "./fs.js";
 import { daemonHttpUrl, resolveMcpServerEntry, assertTokenTransportIsSafe } from "./mcp.js";
-import { hasCodesiftHook, loadHooksSection } from "./hooks.js";
+import { hasCodesiftHook, loadHooksSection, saveHooksSection } from "./hooks.js";
 export function stripCodesiftToolApprovalOverrides(content) {
     const expression = /\[mcp_servers\.codesift\.tools\.[^\]]+\][\t ]*\r?\napproval_mode[\t ]*=[\t ]*"[^"]*"[\t ]*\r?\n?/g;
     const matches = content.match(expression);
@@ -75,7 +75,10 @@ function getCodexServerEntryLines(options) {
     if (options?.http) {
         // Same guard as the JSON path: a token on a plaintext non-loopback URL is refused.
         assertTokenTransportIsSafe(options);
-        const lines = ["url = " + jsonString(daemonHttpUrl(options.port, options.cwd, options.host, options.scheme))];
+        // `client=codex` is what lets the daemon front-load for THIS client without changing the list
+        // every other client sees — Codex freezes its tool list at session start, so a tool not offered
+        // up front is unreachable for the whole session.
+        const lines = ["url = " + jsonString(daemonHttpUrl(options.port, options.cwd, options.host, options.scheme, options.client ?? "codex"))];
         if (options.token) {
             lines.push("[mcp_servers.codesift.http_headers]");
             lines.push("Authorization = " + jsonString(`Bearer ${options.token}`));
@@ -124,8 +127,14 @@ function normalizeCodesiftTomlServerEntry(content, options) {
     const hasNpxCommand = /^command[\t ]*=[\t ]*"[^"]*npx"/m.test(block);
     const argsCarryPackage = /^args[\t ]*=.*codesift-mcp/m.test(block);
     const hasLegacyNpx = hasNpxCommand && !argsCarryPackage;
+    // An HTTP entry written before per-client tool lists existed carries no `client=`, and without it
+    // the daemon cannot tell a frozen-list host from any other — Codex silently gets the small core
+    // list and its reveal-dependent tools are unreachable for the whole session. Equivalence used to
+    // be "is it HTTP at all", so `setup --http` reported `already configured` and left every existing
+    // install on the broken shape, `--force` included.
+    const httpMissingClient = hasHttp && !/^url[\t ]*=[\t ]*"[^"]*[?&]client=/m.test(block);
     const shouldRewrite = desiredHttp !== hasHttp ||
-        (desiredHttp ? hasStdio : hasHttp || hasLegacyNpx || hasDistServer);
+        (desiredHttp ? hasStdio || httpMissingClient : hasHttp || hasLegacyNpx || hasDistServer);
     if (!shouldRewrite)
         return { content, changed: false };
     const withoutEntry = block.replace(/^(command|args|url)[\t ]*=.*(?:\r?\n)?/gm, "");
@@ -142,17 +151,103 @@ function normalizeCodesiftTomlServerEntry(content, options) {
         changed: true,
     };
 }
+/**
+ * Remove `[mcp_servers.codesift.env]` when the entry is HTTP.
+ *
+ * Env vars configure a process this client no longer spawns — under HTTP the daemon carries its
+ * own environment. Codex does not ignore the leftover, it refuses the whole file:
+ *
+ *     Error loading config.toml: env is not supported for streamable_http
+ *
+ * Verified against codex-cli 0.144.6. Leaving it behind means `setup --http` writes a config the
+ * client cannot load at all, which is worse than not converting: every MCP server in the file goes
+ * down with it, not just codesift.
+ */
+function stripCodesiftEnvTable(content) {
+    const header = "[mcp_servers.codesift.env]";
+    const start = content.indexOf(header);
+    if (start === -1)
+        return { content, changed: false };
+    const after = start + header.length;
+    const nextTable = content.slice(after).search(/\n\[[^\]]+\]/);
+    const end = nextTable === -1 ? content.length : after + nextTable;
+    const before = content.slice(0, start).replace(/\n+$/, "\n");
+    return { content: before + content.slice(end).replace(/^\n+/, "\n"), changed: true };
+}
+/**
+ * Keep a project-scoped config out of the repository's history.
+ *
+ * The file pins an ABSOLUTE path (`?cwd=/Users/someone/DEV/thing`), so committing it hands every
+ * other developer a URL pointing at a directory that does not exist on their machine. Left
+ * untracked and unignored it also shows up in `git status` forever, which is how it eventually gets
+ * committed by accident.
+ *
+ * Written to `.git/info/exclude`, never to `.gitignore`: the exclusion is a fact about THIS
+ * checkout, and editing a tracked file to accommodate a local tool is a change the repo's owners
+ * did not ask for. Best-effort — a failure here must not fail the setup.
+ */
+async function excludeProjectConfigLocally(projectRoot) {
+    try {
+        const excludePath = join(projectRoot, ".git", "info", "exclude");
+        if (!existsSync(join(projectRoot, ".git")))
+            return false;
+        const current = existsSync(excludePath) ? await readFile(excludePath, "utf-8") : "";
+        if (/^\.codex\/?$/m.test(current))
+            return false;
+        await ensureDir(join(projectRoot, ".git", "info"));
+        const sep = current.length === 0 || current.endsWith("\n") ? "" : "\n";
+        await writeFile(excludePath, `${current}${sep}# codesift: per-project MCP config pins an absolute path\n.codex/\n`);
+        return true;
+    }
+    catch {
+        return false;
+    }
+}
 export async function setupCodex(options) {
-    const configDir = join(homedir(), ".codex");
+    // Codex merges a project's .codex/config.toml INTO the global one rather than replacing it, and
+    // the merge is per key. So a project entry carrying `url` lands on a global entry that already
+    // carries `command`, and Codex refuses the result outright:
+    //
+    //     Error loading config.toml: url is not supported for stdio in `mcp_servers.codesift`
+    //
+    // Verified against codex-cli 0.144.6. The consequence is that a project-scoped HTTP entry cannot
+    // coexist with a global STDIO one — the global entry has to be HTTP too (a bare daemon URL with
+    // no ?cwd=, which each project then overrides with its own).
+    const projectScope = options?.projectScope === true;
+    const projectRoot = options?.cwd ?? process.cwd();
+    const configDir = projectScope ? join(projectRoot, ".codex") : join(homedir(), ".codex");
     const configPath = join(configDir, "config.toml");
+    if (projectScope) {
+        const globalToml = join(homedir(), ".codex", "config.toml");
+        if (existsSync(globalToml)) {
+            const g = await readFile(globalToml, "utf-8");
+            const block = extractCodesiftTomlBlock(g);
+            if (block && /^(command|args)[\t ]*=/m.test(block.block)) {
+                throw new Error("The global ~/.codex/config.toml still defines mcp_servers.codesift as stdio "
+                    + "(`command = ...`). Codex MERGES the project config into it, so this project's `url` "
+                    + "would produce `url is not supported for stdio` and Codex would refuse to start. "
+                    + "Convert the global entry first: `codesift setup codex --http` (no --project), which "
+                    + "writes a bare daemon URL that each project's config then overrides.");
+            }
+        }
+    }
     await ensureDir(configDir);
+    // Runs on every path, not only on creation: a config written before this existed is exactly the
+    // one still sitting unignored in someone's `git status`.
+    if (projectScope)
+        await excludeProjectConfigLocally(projectRoot);
     if (!existsSync(configPath)) {
         await writeSecretFile(configPath, getCodexTomlBlock(options).trimStart());
         return { platform: "codex", config_path: configPath, status: "created" };
     }
     const original = await readFile(configPath, "utf-8");
     const { content: cleaned, removed } = stripCodesiftToolApprovalOverrides(original);
-    const normalizedEntry = normalizeCodesiftTomlServerEntry(cleaned, options);
+    // Strip the env sub-table BEFORE normalising: an HTTP entry that keeps it makes Codex refuse the
+    // entire config file, taking every other MCP server down with it.
+    const envStripped = options?.http === true
+        ? stripCodesiftEnvTable(cleaned)
+        : { content: cleaned, changed: false };
+    const normalizedEntry = normalizeCodesiftTomlServerEntry(envStripped.content, options);
     const normalized = ensureCodesiftDefaultToolsApprovalApprove(normalizedEntry.content);
     const required = ensureCodesiftRequired(normalized.content);
     const content = required.content;
@@ -160,7 +255,7 @@ export async function setupCodex(options) {
         ? { note: "removed " + removed + " per-tool approval override" + (removed === 1 ? "" : "s") + " on mcp_servers.codesift" }
         : {};
     if (content.includes("[mcp_servers.codesift]")) {
-        if (removed > 0 || normalized.changed || normalizedEntry.changed || required.changed) {
+        if (removed > 0 || envStripped.changed || normalized.changed || normalizedEntry.changed || required.changed) {
             await writeSecretFile(configPath, content);
             return { platform: "codex", config_path: configPath, status: "updated", ...noteFields };
         }
@@ -173,7 +268,7 @@ export async function setupCodexHooks() {
     const configDir = process.env["CODEX_HOME"] ?? join(homedir(), ".codex");
     const hooksPath = join(configDir, "hooks.json");
     await ensureDir(configDir);
-    const { root, hooks } = await loadHooksSection(hooksPath);
+    const { root, hooks, original } = await loadHooksSection(hooksPath);
     for (const event of Object.keys(hooks)) {
         const entries = hooks[event];
         if (!Array.isArray(entries))
@@ -184,6 +279,6 @@ export async function setupCodexHooks() {
         else
             hooks[event] = kept;
     }
-    await writeJsonFile(hooksPath, root);
+    await saveHooksSection(hooksPath, root, original);
 }
 //# sourceMappingURL=codex.js.map