MCP server configured but its tools don't show up in the client (Claude Code, Claude Desktop, other MCP clients). How do I check the config path, JSON syntax, absolute paths and restart?

Cause: The usual reasons are a config file in a place the client does not read, invalid JSON, a command that is not found because the client launches it with a different PATH or working directory, a server that exits at startup, or a client that was not restarted after the change. The MCP debugging guide lists the common startup problems as path issues (wrong executable path, missing files, permissions), configuration errors (invalid JSON, missing fields, type mismatches) and environment problems (missing variables). Fix (best first): 1. Check the server status in the client. In Claude Code run /mcp inside a session, or claude mcp list and claude mcp get <name> in a shell; they show connected, failed or pending-approval states. Project servers in .mcp.json need approval in an interactive session. 2. Make sure you edited the file the client actually reads. Claude Code documents three scopes: local and user (stored in ~/.claude.json) and project (.mcp.json in the project root). If the same server name appears in several scopes, one definition wins and fields are not merged. Other clients have their own file locations; check their docs. 3. Validate the JSON (for example python3 -m json.tool < config.json). Trailing commas and comments are errors. 4. Use absolute paths. The MCP guide says the working directory for servers started from a client config may be undefined, so relative paths such as ./data can fail. Use an absolute path for the command if the client cannot find it. 5. Servers started over stdio inherit only a limited set of environment variables; pass what the server needs in the env key instead of relying on your shell. 6. For Claude Code, add stdio servers with the server command after a double dash, for example: claude mcp add --transport stdio myserver -- npx -y some-mcp-server. Without the double dash, the server's own flags can be parsed as Claude's options. 7. Restart the client after configuration changes. For Claude Desktop the guide says to fully quit and reopen, since closing the window is not enough. 8. Test the server alone with the MCP Inspector to separate a server bug from a client config problem, and read the client logs. Don't: put API keys directly into a config file that is committed to version control. Verify: /mcp (or claude mcp list) shows the server as connected and its tools appear in the client's tool list. Sources: https://modelcontextprotocol.io/docs/tools/debugging https://code.claude.com/docs/en/mcp