diff --git a/cspell.json b/cspell.json
index 55f2404b5..0b223847e 100644
--- a/cspell.json
+++ b/cspell.json
@@ -104,6 +104,7 @@
     "eabi",
     "eamodio",
     "eastasianwidth",
+    "elicitations",
     "émøjî",
     "éñüñ",
     "encodeurl",
diff --git a/docs/reference/file-formats.md b/docs/reference/file-formats.md
index db464246e..f13671582 100644
--- a/docs/reference/file-formats.md
+++ b/docs/reference/file-formats.md
@@ -277,6 +277,8 @@ Execute the following in parallel:
 
 The command body itself uses a Claude Code-compatible **universal syntax** (e.g. `$ARGUMENTS`, `` !`cmd` ``). When a target tool expects a different placeholder syntax, rulesync translates it automatically on generation and reverses the translation on import. See [Command Syntax](./command-syntax.md) for the full mapping.
 
+> **Codex CLI deprecation note:** Codex CLI's own docs now state "Custom prompts are deprecated. Use skills for reusable instructions" (see [Custom Prompts](https://developers.openai.com/codex/custom-prompts)). Rulesync's `codexcli` commands still generate the global-only `~/.codex/prompts/*.md` custom-prompt files described above — they remain functional and no removal date has been announced, so this behavior is unchanged for now. For new reusable instructions, prefer rulesync's `codexcli` skills support (see `.rulesync/skills/*/SKILL.md` below) instead.
+
 > **Qwen Code note:** Custom commands are emitted as **Markdown** files (not TOML — TOML is deprecated upstream) under `.qwen/commands/` (project) and `~/.qwen/commands/` (global, via `--global`). The file is an optional YAML frontmatter block (`description`) followed by the prompt body. Subdirectory namespacing is supported: `.qwen/commands/git/commit.md` becomes the `/git:commit` command. Any extra fields are preserved on round-trip under the `qwencode:` block.
 
 > **OpenCode import note:** OpenCode lets commands live both as Markdown files under `.opencode/commands/*.md` **and** inline in `opencode.json`/`opencode.jsonc` under the top-level `command` key. On import, rulesync reads both: each inline entry's `template` becomes the command body and its `description`/`agent`/`model`/`subtask` fields become frontmatter. A Markdown file takes precedence over an inline entry with the same name.
diff --git a/skills/rulesync/file-formats.md b/skills/rulesync/file-formats.md
index db464246e..f13671582 100644
--- a/skills/rulesync/file-formats.md
+++ b/skills/rulesync/file-formats.md
@@ -277,6 +277,8 @@ Execute the following in parallel:
 
 The command body itself uses a Claude Code-compatible **universal syntax** (e.g. `$ARGUMENTS`, `` !`cmd` ``). When a target tool expects a different placeholder syntax, rulesync translates it automatically on generation and reverses the translation on import. See [Command Syntax](./command-syntax.md) for the full mapping.
 
+> **Codex CLI deprecation note:** Codex CLI's own docs now state "Custom prompts are deprecated. Use skills for reusable instructions" (see [Custom Prompts](https://developers.openai.com/codex/custom-prompts)). Rulesync's `codexcli` commands still generate the global-only `~/.codex/prompts/*.md` custom-prompt files described above — they remain functional and no removal date has been announced, so this behavior is unchanged for now. For new reusable instructions, prefer rulesync's `codexcli` skills support (see `.rulesync/skills/*/SKILL.md` below) instead.
+
 > **Qwen Code note:** Custom commands are emitted as **Markdown** files (not TOML — TOML is deprecated upstream) under `.qwen/commands/` (project) and `~/.qwen/commands/` (global, via `--global`). The file is an optional YAML frontmatter block (`description`) followed by the prompt body. Subdirectory namespacing is supported: `.qwen/commands/git/commit.md` becomes the `/git:commit` command. Any extra fields are preserved on round-trip under the `qwencode:` block.
 
 > **OpenCode import note:** OpenCode lets commands live both as Markdown files under `.opencode/commands/*.md` **and** inline in `opencode.json`/`opencode.jsonc` under the top-level `command` key. On import, rulesync reads both: each inline entry's `template` becomes the command body and its `description`/`agent`/`model`/`subtask` fields become frontmatter. A Markdown file takes precedence over an inline entry with the same name.
diff --git a/src/features/commands/codexcli-command.ts b/src/features/commands/codexcli-command.ts
index ba0765ebd..a7174ca1e 100644
--- a/src/features/commands/codexcli-command.ts
+++ b/src/features/commands/codexcli-command.ts
@@ -30,6 +30,16 @@ export type CodexcliCommandParams = {
   body: string;
 } & Omit<AiFileParams, "fileContent">;
 
+/**
+ * Generates Codex CLI's global-only custom prompts under `~/.codex/prompts/*.md`.
+ *
+ * Note: upstream Codex docs now state "Custom prompts are deprecated. Use skills for
+ * reusable instructions" (https://developers.openai.com/codex/custom-prompts). No removal
+ * date has been announced and custom prompts remain functional, so this class's
+ * generation behavior is unchanged. Prefer rulesync's `codexcli` skills support
+ * (see `src/features/skills/codexcli-skill.ts`) for new reusable instructions going
+ * forward; this class is kept for users who still rely on custom prompts.
+ */
 export class CodexcliCommand extends ToolCommand {
   private readonly frontmatter: CodexcliCommandFrontmatter;
   private readonly body: string;
diff --git a/src/features/hooks/codexcli-hooks.test.ts b/src/features/hooks/codexcli-hooks.test.ts
index 74f5c4560..96432e316 100644
--- a/src/features/hooks/codexcli-hooks.test.ts
+++ b/src/features/hooks/codexcli-hooks.test.ts
@@ -532,9 +532,9 @@ describe("CodexcliConfigToml", () => {
     await cleanup();
   });
 
-  it("should generate config.toml with hooks feature flag", async () => {
+  it("should not force-write [features] hooks = true (hooks are GA/default-on)", async () => {
     const configToml = await CodexcliConfigToml.fromOutputRoot({ outputRoot: testDir });
-    expect(configToml.getFileContent()).toContain("hooks = true");
+    expect(configToml.getFileContent()).not.toContain("hooks = true");
     expect(configToml.getFileContent()).not.toContain("codex_hooks");
   });
 
@@ -547,23 +547,36 @@ describe("CodexcliConfigToml", () => {
 
     const configToml = await CodexcliConfigToml.fromOutputRoot({ outputRoot: testDir });
     const content = configToml.getFileContent();
-    expect(content).toContain("hooks = true");
+    expect(content).not.toContain("hooks = true");
     expect(content).not.toContain("codex_hooks");
     expect(content).toContain("mcp_servers");
     expect(content).toContain("myserver");
   });
 
-  it("should preserve existing [features] values when enabling hooks", async () => {
+  it("should preserve existing [features] values without adding hooks = true", async () => {
     await ensureDir(join(testDir, ".codex"));
     await writeFileContent(join(testDir, ".codex", "config.toml"), "[features]\nverbose = true\n");
 
+    const configToml = await CodexcliConfigToml.fromOutputRoot({ outputRoot: testDir });
+    const content = configToml.getFileContent();
+    expect(content).not.toContain("hooks = true");
+    expect(content).toContain("verbose = true");
+  });
+
+  it("should not strip a user-set [features] hooks = true value", async () => {
+    await ensureDir(join(testDir, ".codex"));
+    await writeFileContent(
+      join(testDir, ".codex", "config.toml"),
+      "[features]\nhooks = true\nverbose = true\n",
+    );
+
     const configToml = await CodexcliConfigToml.fromOutputRoot({ outputRoot: testDir });
     const content = configToml.getFileContent();
     expect(content).toContain("hooks = true");
     expect(content).toContain("verbose = true");
   });
 
-  it("should remove deprecated codex_hooks when enabling hooks", async () => {
+  it("should remove deprecated codex_hooks without adding hooks = true", async () => {
     await ensureDir(join(testDir, ".codex"));
     await writeFileContent(
       join(testDir, ".codex", "config.toml"),
@@ -572,7 +585,7 @@ describe("CodexcliConfigToml", () => {
 
     const configToml = await CodexcliConfigToml.fromOutputRoot({ outputRoot: testDir });
     const content = configToml.getFileContent();
-    expect(content).toContain("hooks = true");
+    expect(content).not.toContain("hooks = true");
     expect(content).toContain("verbose = true");
     expect(content).not.toContain("codex_hooks");
   });
diff --git a/src/features/hooks/codexcli-hooks.ts b/src/features/hooks/codexcli-hooks.ts
index 47c0f0710..087b2d68a 100644
--- a/src/features/hooks/codexcli-hooks.ts
+++ b/src/features/hooks/codexcli-hooks.ts
@@ -37,9 +37,15 @@ const CODEXCLI_CONVERTER_CONFIG: ToolHooksConverterConfig = {
 };
 
 /**
- * Build the content for `.codex/config.toml` with `[features] hooks = true`.
- * Reads the existing file (if any), parses TOML, sets the flag, and returns the content
- * without writing to disk. The caller is responsible for writing via the normal write phase.
+ * Build the content for `.codex/config.toml`, cleaning up the deprecated `codex_hooks` key.
+ * Reads the existing file (if any), parses TOML, and returns the content without writing to
+ * disk. The caller is responsible for writing via the normal write phase.
+ *
+ * Hooks are GA and enabled by default in Codex CLI, so `[features] hooks = true` is no longer
+ * required and is intentionally NOT force-written here (doing so used to be harmless/idempotent,
+ * but is now redundant and could mask a user's own `hooks = false` opt-out on a later edit).
+ * See https://developers.openai.com/codex/hooks. Only the legacy `codex_hooks` alias — superseded
+ * by `hooks` — is still cleaned up.
  */
 async function buildCodexConfigTomlContent({
   outputRoot,
@@ -60,12 +66,9 @@ async function buildCodexConfigTomlContent({
     );
   }
 
-  if (typeof configToml.features !== "object" || configToml.features === null) {
-    configToml.features = {} as smolToml.TomlTable;
+  if (typeof configToml.features === "object" && configToml.features !== null) {
+    delete (configToml.features as smolToml.TomlTable).codex_hooks;
   }
-  const features = configToml.features as smolToml.TomlTable;
-  delete features.codex_hooks;
-  features.hooks = true;
 
   return smolToml.stringify(configToml);
 }
diff --git a/src/features/permissions/codexcli-permissions.test.ts b/src/features/permissions/codexcli-permissions.test.ts
index 3006145c4..40e0eb1c6 100644
--- a/src/features/permissions/codexcli-permissions.test.ts
+++ b/src/features/permissions/codexcli-permissions.test.ts
@@ -1080,6 +1080,72 @@ default_permissions = "rulesync"
     }
   });
 
+  it("should preserve granular tool-approval keys (default_tools_approval_mode, approval_policy, approvals_reviewer, apps.*, mcp_servers.*) on round-trip", async () => {
+    const codexDir = join(testDir, ".codex");
+    await ensureDir(codexDir);
+    await writeFileContent(
+      join(codexDir, "config.toml"),
+      `
+default_tools_approval_mode = "prompt"
+approvals_reviewer = "auto_review"
+
+[approval_policy]
+sandbox_approval = true
+rules = true
+mcp_elicitations = false
+request_permissions = true
+skill_approval = false
+
+[apps.myapp]
+default_tools_approval_mode = "auto"
+
+[mcp_servers.myserver]
+default_tools_approval_mode = "approve"
+command = "node"
+`,
+    );
+
+    const rulesyncPermissions = new RulesyncPermissions({
+      outputRoot: testDir,
+      relativeDirPath: ".rulesync",
+      relativeFilePath: "permissions.json",
+      fileContent: JSON.stringify({
+        permission: {
+          read: { "src/**": "allow" },
+        },
+      }),
+    });
+
+    const codexPermissions = await CodexcliPermissions.fromRulesyncPermissions({
+      outputRoot: testDir,
+      rulesyncPermissions,
+    });
+
+    const fileContent = codexPermissions.getFileContent();
+    const parsed = smolToml.parse(fileContent) as Record<string, unknown>;
+
+    expect(parsed.default_tools_approval_mode).toBe("prompt");
+    expect(parsed.approvals_reviewer).toBe("auto_review");
+    expect(parsed.approval_policy).toEqual({
+      sandbox_approval: true,
+      rules: true,
+      mcp_elicitations: false,
+      request_permissions: true,
+      skill_approval: false,
+    });
+    expect((parsed.apps as Record<string, unknown>).myapp).toEqual({
+      default_tools_approval_mode: "auto",
+    });
+    expect((parsed.mcp_servers as Record<string, unknown>).myserver).toEqual({
+      default_tools_approval_mode: "approve",
+      command: "node",
+    });
+
+    // The rulesync-managed profile is still written alongside the preserved keys.
+    expect(fileContent).toContain('default_permissions = "rulesync"');
+    expect(fileContent).toContain('"src/**" = "read"');
+  });
+
   it("should convert rulesync bash permissions to Codex CLI .rules file", () => {
     const rulesFile = createCodexcliBashRulesFile({
       outputRoot: testDir,
diff --git a/src/features/permissions/codexcli-permissions.ts b/src/features/permissions/codexcli-permissions.ts
index cd7596648..40f49ed55 100644
--- a/src/features/permissions/codexcli-permissions.ts
+++ b/src/features/permissions/codexcli-permissions.ts
@@ -110,6 +110,13 @@ export class CodexcliPermissions extends ToolPermissions {
     const paths = this.getSettablePaths({ global });
     const filePath = join(outputRoot, paths.relativeDirPath, paths.relativeFilePath);
     const existingContent = (await readFileContentOrNull(filePath)) ?? smolToml.stringify({});
+    // `parsed` is a shallow copy of the FULL top-level config.toml table (see toMutableTable),
+    // and only its `permissions` and `default_permissions` keys are overwritten below. This means
+    // Codex config keys rulesync does not model — e.g. the granular tool-approval surface
+    // (`default_tools_approval_mode`, `approval_policy`, `approvals_reviewer`, and their
+    // `apps.<id>.*` / `mcp_servers.<id>.*` variants) — survive a read-modify-write round-trip
+    // untouched, the same way amp/devin permissions preserve sibling settings they don't manage.
+    // https://developers.openai.com/codex/config-reference
     const parsed = toMutableTable(smolToml.parse(existingContent));
 
     const newProfile = convertRulesyncToCodexProfile({