Debug your configuration changeddebug-your-config
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3838Settings merge across managed, user, project, and local scopes. Managed settings apply first when present. Among the rest, the closer scope overrides the broader one in the order local, then project, then user. Some settings can also be set by command-line flags or [environment variables](/docs/en/env-vars), which act as another override layer. When a setting doesn't seem to apply, the value you set is usually being overridden by another scope or an environment variable.
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40Run `/doctor` to check your configuration and installation. It reports what it finds, including invalid settings files, duplicate installations, unused extensions, and checked-in `CLAUDE.md` content Claude can derive from the codebase, then proposes fixes it applies only after you confirm. The `CLAUDE.md` trim check requires Claude Code v2.1.206 or later. Before v2.1.205, `/doctor` opened a read-only diagnostics screen and pressing `f` sent the report to Claude to fix.
40Run [`/doctor`](/docs/en/commands#all-commands) to find invalid settings files.
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4242From the terminal, `claude doctor` prints read-only installation and settings diagnostics without starting a session.
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102102| Subdirectory `CLAUDE.md` instructions seem ignored | Subdirectory files load on demand, not at session start | They load when Claude reads a file in that directory with the Read tool, not at launch and not when writing or creating files there. See [how CLAUDE.md files load](/docs/en/memory#how-claude-md-files-load). |
103103| Subagent ignores `CLAUDE.md` instructions | The built-in Explore and Plan agents skip `CLAUDE.md`. Custom subagents load it the same way the main conversation does | For Explore or Plan, restate the instruction in your delegating prompt. For a custom subagent, put critical instructions in the agent file body, which becomes the agent's system prompt. See [what loads at startup](/docs/en/sub-agents#what-loads-at-startup). |
104104| Cleanup logic never runs at session end | No `SessionEnd` hook configured | Add a `SessionEnd` hook in `settings.json`. See the [hook events list](/docs/en/hooks#hook-events). |
105| MCP servers in `.mcp.json` never load | File is under `.claude/` or uses Claude Desktop's config format | Project MCP config goes at the repository root as `.mcp.json`, not inside `.claude/`. See [MCP configuration](/docs/en/mcp). |
105| MCP servers in `.mcp.json` never load | File is under `.claude/`, or its servers sit under a top-level `servers` key, as in VS Code's `mcp.json`, instead of `mcpServers` | Project MCP config goes at the repository root as `.mcp.json`, not inside `.claude/`, with servers under the `mcpServers` key. See [MCP configuration](/docs/en/mcp). |
106106| MCP servers added under `mcpServers` in `settings.json` never appear | `settings.json` does not read an `mcpServers` key | Define project servers in `.mcp.json` at the repository root, or run `claude mcp add --scope user` for user-scoped servers. See [MCP configuration](/docs/en/mcp). |
107107| Project MCP server added but doesn't appear | The one-time approval prompt was dismissed | Project-scoped servers require approval. Run `/mcp` to see status and approve. |
108108| MCP server fails to start from some directories | `command` or `args` uses a relative file path | Use absolute paths for local scripts. Executables on your `PATH` like `npx` or `uvx` work as-is. |
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