fix(agent-environment): advertise MCP client roots during list_tools

[Abhishek21g]

Summary

• Register FastMCP client roots (default /data) so filesystem-related MCP servers get a timely roots/list response instead of timing out or logging List roots not supported.
• Add parse_client_roots() with unit tests and document MCP_CLIENT_ROOTS in env.template.

Fixes #17, #18

Problem

During eval startup, MCP servers (notably filesystem) request initial roots from the client. The agent-environment Client was created without a roots handler, which produces intermittent:

Failed to request initial roots from client: MCP error -32001: Request timed out
Failed to request initial roots from client: MCP error -32603: List roots not supported

This can slow or destabilize list_tools when many servers start concurrently.

Solution

Pass roots=parse_client_roots() to fastmcp.Client. Default is /data, matching desktop-commander allowedDirectories and filesystem paths in mcp_server_template.json. Override via comma-separated MCP_CLIENT_ROOTS.

Test plan

• cd services/agent-environment && PYTHONPATH=src python3 -m pytest tests/test_client_roots.py tests/test_mcp_config_sync.py -v
• make build && make run-docker with ENABLED_SERVERS=filesystem,git — confirm no roots timeout spam in logs during startup
• curl -X POST http://localhost:1984/list-tools succeeds

Greptile Summary

This PR fixes intermittent roots/list timeout errors during list_tools startup by registering filesystem roots with the fastmcp.Client. It adds a small, focused parse_client_roots() helper, wires it into mcp_client.py, and documents the MCP_CLIENT_ROOTS env var. Previously flagged issues (hardcoded default in os.getenv, env isolation in tests) have both been resolved.

• client_roots.py: New module with DEFAULT_CLIENT_ROOTS = ["/data"] and parse_client_roots() that correctly references the constant as the os.getenv fallback, with a safe empty-list guard.
• mcp_client.py: Calls parse_client_roots() at module level and passes the result to Client(roots=...), which FastMCP accepts as a list[str] and converts to mcp.types.Root objects internally.
• test_client_roots.py: Covers default, single, multi-root, and whitespace-stripping cases; a test for the env-var-is-set code path is missing but the rest of the logic is well validated.

Confidence Score: 5/5

Safe to merge — the change is additive, touches only startup initialization, and both previously reported issues have been corrected.

The new code is small and isolated: a pure-function parser, a module-level call that reads an env var at startup, and a single extra kwarg on the existing Client constructor. FastMCP documents list[str] as a valid roots input and handles the conversion to mcp.types.Root internally. There are no data-path or auth changes, and the fix directly addresses a known startup race condition.

No files require special attention. The only gap is a missing test for the env-var-is-set code path in test_client_roots.py, but the runtime behavior is straightforward.

Important Files Changed

Filename	Overview
services/agent-environment/src/agent_environment/client_roots.py	New module exposing parse_client_roots() with correct DEFAULT_CLIENT_ROOTS reference in the os.getenv fallback and a safe fallback when the parsed list is empty.
services/agent-environment/src/agent_environment/mcp_client.py	Adds module-level parse_client_roots() call and passes the result as roots= to fastmcp.Client; logger is already initialised at line 11, so the new logger.info call is safe.
services/agent-environment/tests/test_client_roots.py	Unit tests cover default fallback (with env deletion via monkeypatch), single root, multiple roots, and whitespace stripping; the env-var-is-set path for parse_client_roots(None) is not tested but the core logic is validated.
env.template	Documents MCP_CLIENT_ROOTS in the correct section with a commented-out example and a clear description of the default.
services/agent-environment/README.md	Adds one sentence explaining the roots advertised to MCP servers and links to the relevant issues; no inaccuracies.

Sequence Diagram

%%{init: {'theme': 'neutral'}}%%
sequenceDiagram
    participant E as Environment (MCP_CLIENT_ROOTS)
    participant CR as client_roots.py
    participant MC as mcp_client.py (module init)
    participant FC as fastmcp.Client
    participant MS as MCP Server (e.g. filesystem)

    MC->>CR: parse_client_roots()
    CR->>E: os.getenv("MCP_CLIENT_ROOTS", "/data")
    E-->>CR: "/data" (or custom paths)
    CR-->>MC: ["/data"]
    MC->>FC: "Client(config, roots=["/data"])"
    Note over FC: converts str to mcp.types.Root(uri=FileUrl)
    MS->>FC: roots/list request
    FC-->>MS: "[Root(uri="file:///data")]"

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sequenceDiagram
    participant E as Environment (MCP_CLIENT_ROOTS)
    participant CR as client_roots.py
    participant MC as mcp_client.py (module init)
    participant FC as fastmcp.Client
    participant MS as MCP Server (e.g. filesystem)

    MC->>CR: parse_client_roots()
    CR->>E: os.getenv("MCP_CLIENT_ROOTS", "/data")
    E-->>CR: "/data" (or custom paths)
    CR-->>MC: ["/data"]
    MC->>FC: "Client(config, roots=["/data"])"
    Note over FC: converts str to mcp.types.Root(uri=FileUrl)
    MS->>FC: roots/list request
    FC-->>MS: "[Root(uri="file:///data")]"

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