docs(code): document saved project MCP approvals

[Mason Daugherty (mdrxy)]

Deep Agents Code 0.1.40 replaced persisted whole-project MCP trust with selective approvals scoped to the project root, server name, and server-definition fingerprint. The documentation still described the removed mcp_trust.json store and treated project trust as stdio-only, which could lead users to stale configuration and cleanup steps.

This update explains the allow-once and saved-approval flows, the allow and deny precedence rules, the restrictions on project .env files, and the migration from the legacy TOML key and environment variable. It also corrects the MCP login option to --mcp-config and aligns the CLI reference with remote-server trust gating.

Type of change

Type: Update existing documentation

Related issues/PRs

• Feature PR: feat(code): add "always allow" to project MCP approval prompt deepagents#4562

Checklist

• I have read the contributing guidelines, including the language policy
• I have tested my changes locally using docs dev
• All code examples have been tested and work correctly
• I have used root relative paths for internal links
• I have updated navigation in src/docs.json if needed

[github-actions]

Mintlify preview branch generated: preview-docsde-1784577418-f712cd8

Site preview: https://langchain-5e9cc07a-preview-docsde-1784577418-f712cd8.mintlify.site

Important

Preview links may take a few minutes to start working while the deployment finishes.

Changed documentation pages (preview deep links):

• src/oss/deepagents/code/mcp-tools.mdx
• src/oss/deepagents/code/configuration.mdx
• src/oss/deepagents/code/cli-reference.mdx