Cline configuration guide: instruction files, MCP, permissions

Cline Bot Inc. · IDE / editor · CLI · verified against official docs on 2026-10-12

Cline reads workspace rules from .clinerules/ or .cline/rules/, global rules from ~/Documents/Cline/Rules, and also detects .cursorrules, .windsurfrules, AGENTS.md and ~/.agents/AGENTS.md. MCP servers are stored in Cline's cline_mcp_settings.json. Auto Approve toggles control reads, edits and commands. You can use a Claude Pro/Max plan through the Claude Code provider (it calls your installed, logged-in Claude CLI) or a ChatGPT plan through the OpenAI Codex sign-in provider.

Cline at a glance

Global instructions✓ Yes
~/Documents/Cline/Rules (also ~/.cline/rules), ~/.agents/AGENTS.md
Project instructions✓ Yes
.clinerules/ or .cline/rules/; auto-detects .cursorrules, .windsurfrules, AGENTS.md
Nested / subfolder? Not documented
Not documented
AGENTS.md✓ Yes
AGENTS.md and global ~/.agents/AGENTS.md
Skills (SKILL.md)✓ Yes
.cline/skills/ (recommended), .clinerules/skills/, .claude/skills/; global ~/.cline/skills/
MCP config✓ Yes
IDE: MCP Servers → Configure → cline_mcp_settings.json (mcpServers). CLI: ~/.cline/data/settings/cline_mcp_settings.json
Permissions / allowlist◐ Partial
Auto Approve per category (read, edit, safe commands, all commands) and YOLO mode; the model flags commands as requiring approval, no fixed allowlist
Sandbox? Not documented
Not documented for the local extension
Hooks◐ Partial
Lifecycle hooks via plugins
Claude Pro/Max login✓ Yes
Claude Code provider: uses your Claude Pro/Max limits via the installed, logged-in Claude CLI
ChatGPT Plus/Pro login✓ Yes
OpenAI Codex provider: sign in with your ChatGPT account (OAuth)
API key / own plan✓ Yes
Anthropic, OpenAI, OpenRouter, Bedrock, Gemini and many more providers

Exact file paths

PathScopeWhat it does
.clinerules/ or .cline/rules/WorkspaceRule markdown files
~/Documents/Cline/RulesUserGlobal rules
AGENTS.md / ~/.agents/AGENTS.mdWorkspace / userCross-tool instructions
.cursorrules / .windsurfrulesWorkspaceDetected automatically
cline_mcp_settings.jsonUserMCP servers (CLI: ~/.cline/data/settings/)
.cline/skills/<name>/SKILL.mdWorkspaceSkills (global: ~/.cline/skills/)

Using a shared AGENTS.md with Cline

Native: AGENTS.md is detected automatically. See one AGENTS.md for every agent, or generate one with the AGENTS.md generator.

Copy-paste examples

Workspace rule

File: .clinerules/testing.md

# Testing

- Run `pytest -q` after every change to `app/`.
- Never edit files under `migrations/` without asking.

Safe permissions preset

Safe Cline Auto Approve settings

File: Cline → Auto Approve

Read project files ............ ON
Read all files ................ OFF   (keeps ~/.ssh, ~/.aws out of reach without asking)
Edit project files ............ ON    (review diffs before committing)
Edit all files ................ OFF
Execute safe commands ......... ON
Execute all commands .......... OFF   (rm -rf, git push --force, psql DROP ... always ask)
Use the browser ............... OFF
Use MCP servers ............... ask per tool
YOLO mode ..................... OFF

Cline has no fixed command allowlist: the model marks each command as safe or requiring approval, so treat "safe commands" as best-effort. Keep "Execute all commands" and YOLO off and add a rule such as "Never run destructive commands; ask first" in .clinerules.

Gotchas

  • Command safety is decided by the model's approval flag, not by a deterministic list.
  • The Claude Code provider runs your installed Claude CLI and uses its subscription limits; some features (such as images) are limited in that mode.
  • Workspace rules win over global rules when they conflict; both are combined.

FAQ

Where are Cline rules stored?
Workspace rules go in .clinerules/ or .cline/rules/ at the project root. Global rules go in ~/Documents/Cline/Rules. Cline also reads AGENTS.md, .cursorrules and .windsurfrules.
Can Cline use my Claude Max subscription?
Yes, through the Claude Code provider: install and log in to the Claude CLI, then pick Claude Code as the provider. Requests use your subscription limits instead of API billing.
Where is the Cline MCP settings file?
Open MCP Servers → Configure → Configure MCP Servers in the extension to edit cline_mcp_settings.json. The CLI uses ~/.cline/data/settings/cline_mcp_settings.json.

Sources

Checked against these official pages on 2026-10-12. Cells marked "Not documented" mean we could not find the behaviour in these docs; it may still exist.