fix(cli): fix test isolation for model-persistence tests

Mock core/util/paths.js to read CONTINUE_GLOBAL_DIR dynamically instead
of caching it at module load time. This fixes test isolation issues where
tests running in parallel would share the same GlobalContext file path.

Root cause: The CONTINUE_GLOBAL_DIR constant in core/util/paths.ts is
computed via an IIFE at module load time. When tests set different temp
directories in beforeEach, the module had already cached the original value.

Solution: Mock getContinueGlobalPath, getIndexFolderPath, and
getGlobalContextFilePath to read process.env.CONTINUE_GLOBAL_DIR on
each call, allowing proper test isolation.

Also fixes prettier formatting in markdown files.

Authored by: Aaron Lippold<lippold@gmail.com>

Author: aaronlippold

extensions/cli/AGENTS.md

@@ -18,30 +18,25 @@ This is a CLI tool for Continue Dev that provides an interactive AI-assisted dev
 ### Core Components
 
 1. **Entry Point** (`src/index.ts`): Main CLI logic with two modes:
-
    - **Headless mode**: Non-interactive mode for automation/CI
    - **TUI mode**: Terminal User Interface using Ink/React
    - **Standard mode**: Traditional readline-based chat interface
 
 2. **Authentication** (`src/auth/`): WorkOS-based authentication system
-
    - `ensureAuth.ts`: Handles authentication flow
    - `workos.ts`: WorkOS configuration and token management
 
 3. **Continue SDK Integration** (`src/continueSDK.ts`): Initializes the Continue SDK client with:
-
    - API key authentication
    - Assistant configuration (slug-based)
    - Organization support
 
 4. **Terminal UI** (`src/ui/`): React/Ink-based TUI components
-
    - `TUIChat.tsx`: Main chat interface component
    - `UserInput.tsx`: Input handling with multi-line support
    - `TextBuffer.ts`: Text display utilities
 
 5. **Tools System** (`src/tools/`): Built-in development tools including:
-
    - File operations (read, write, list)
    - Code search functionality
    - Terminal command execution

extensions/cli/spec/config-loading.md

@@ -23,13 +23,11 @@ This document specifies the behavior of the CLI's configuration loading system,
 **When CLI is invoked, config source is determined in this order:**
 
 1. **CLI `--config` Flag** (highest priority)
-
    - File path (starts with `.`, `/`, `~`): Loads local YAML file
    - Assistant slug (`owner/package`): Fetches from Continue platform
    - Overrides any saved preferences
 
 2. **Saved Config URI** (if no `--config` flag)
-
    - Retrieved from authentication config
    - Converts `file://` URIs back to file paths
    - Converts `slug://` URIs back to assistant slugs

extensions/cli/spec/onboarding.md

@@ -9,7 +9,6 @@ When a user first runs `cn` in interactive mode, they will be taken through "onb
 1. If the --config flag is provided, load this config
 2. If the CONTINUE_USE_BEDROCK environment variable is set to "1", automatically use AWS Bedrock configuration and skip interactive prompts
 3. Present the user with available options:
-
    - Log in with Continue: log them in, which will automatically create their assistant and then we can load the first assistant from the first org
    - Enter your Anthropic API key: let them enter the key, and then either create a ~/.continue/config.yaml with the following contents OR update the existing config.yaml to add the model
 

extensions/cli/vitest.setup.ts

@@ -1,3 +1,6 @@
+import * as fs from "fs";
+import * as path from "path";
+
 import { vi } from "vitest";
 
 import { resetConsoleOverrides } from "./src/init.js";
@@ -6,6 +9,42 @@ import { resetConsoleOverrides } from "./src/init.js";
 process.env.CONTINUE_CLI_ENABLE_TELEMETRY = "0";
 process.env.CONTINUE_ALLOW_ANONYMOUS_TELEMETRY = "0";
 
+// Mock core/util/paths to read CONTINUE_GLOBAL_DIR dynamically
+// This fixes test isolation issues where the module caches the env var at load time
+vi.mock("core/util/paths.js", async (importOriginal) => {
+  const actual = await importOriginal<typeof import("core/util/paths.js")>();
+
+  // Create a dynamic version of getContinueGlobalPath that reads env var each time
+  const getContinueGlobalPath = () => {
+    const continuePath =
+      process.env.CONTINUE_GLOBAL_DIR ||
+      path.join(process.env.HOME || "", ".continue");
+    if (!fs.existsSync(continuePath)) {
+      fs.mkdirSync(continuePath, { recursive: true });
+    }
+    return continuePath;
+  };
+
+  const getIndexFolderPath = () => {
+    const indexPath = path.join(getContinueGlobalPath(), "index");
+    if (!fs.existsSync(indexPath)) {
+      fs.mkdirSync(indexPath, { recursive: true });
+    }
+    return indexPath;
+  };
+
+  const getGlobalContextFilePath = () => {
+    return path.join(getIndexFolderPath(), "globalContext.json");
+  };
+
+  return {
+    ...actual,
+    getContinueGlobalPath,
+    getIndexFolderPath,
+    getGlobalContextFilePath,
+  };
+});
+
 // Mock fetch to prevent actual API calls in tests
 const originalFetch = global.fetch;
 global.fetch = vi