astra mcp list (default project scope) reports no servers while astra chat loads user-level ~/.astra/mcp.json — no effective/merged MCP view

[guolvlin-cn]

Summary

astra mcp list (default scope project) reports "No MCP servers configured." while astra chat loads and connects the user-level ~/.astra/mcp.json servers in the same session. The CLI default hides user-level config, and there is no command that shows the effective/merged set of MCP servers that a chat session actually uses — so users configuring user-level MCP servers get a misleading "nothing configured" from the CLI while chat silently connects them.

Environment

• Commit: 27c0c9e4 (fix(services): decode Edge Registry JSON as text (fix(services): decode Edge Registry JSON as text #615), 2026-08-15)
• Version: astra 0.1.0
• OS: macOS, Rust 1.97 toolchain
• Mode: astra mcp list (CLI) vs astra chat (CLI one-shot)

Reproduction

1. Build + deps (same as #621)

git clone https://github.com/guolvlin-cn/astra   # or matrixorigin/astra @ 27c0c9e4
make build
make dev-init && make dev-deps-up && make dev-api-start
astra admin register --username <u> --password <p> --email <e>

2. Configure user-level MCP servers (the path astra chat honors)

Create ~/.astra/mcp.json:

{
  "mcpServers": {
    "memoria": {
      "type": "stdio",
      "command": "memoria",
      "args": ["mcp", "--tool", "astra", "--api-url", "https://api.thememoria.ai", "--token", "<TOKEN>"]
    },
    "MiniMax": {
      "type": "stdio",
      "command": "uvx",
      "args": ["--with", "mcp<2", "minimax-coding-plan-mcp", "-y"],
      "env": { "MINIMAX_API_KEY": "<KEY>", "MINIMAX_API_HOST": "https://api.minimaxi.com" }
    },
    "playwright": {
      "type": "stdio",
      "command": "npx",
      "args": ["-y", "@playwright/mcp@latest"],
      "env": {}
    }
  }
}

3. Run the CLI listing from a project dir with no project-level mcp.json

cd /Users/guolvlin/astra-workspace
astra mcp list                 # default scope = project
# → "No MCP servers configured."
# → "Use astra mcp add to add a server."

4. Same command with user scope

astra mcp list -s user
# →
#   Name      Type   Command / URL
#   MiniMax   stdio  uvx --with mcp<2 minimax-coding-plan-mcp -y
#   memoria   stdio  memoria mcp --tool astra --api-url https://api.thememoria.ai --token sk-…
#   playwright stdio npx -y @playwright/mcp@latest
#   Config: /Users/guolvlin/.astra/mcp.json

5. Meanwhile, astra chat loads the user-level servers

astra chat -m "hello" --permission-mode bypass --quiet
# startup log:
#   3 MCP servers connected: playwright (24) · MiniMax (2) · memoria (23)

Actual behavior

• astra mcp list with the default project scope reports no servers, even though a user-level ~/.astra/mcp.json exists and is actively used by astra chat.
• There is no single command that shows the effective/merged set of servers a chat session will load (project + skill manifests + user).
• The TUI slash command /mcp list inside a chat session does show the connected set (from McpClientManager::all_tools()), so the two surfaces disagree.

Expected behavior

One of:

• astra mcp list should surface user-level config by default (or clearly indicate scope + hint -s user), and/or
• Provide a way to show the effective merged set that a session will load (e.g. astra mcp list --effective, or a note when user-level servers exist).

Root cause

• astra mcp list / add default to scope project (cli_args): -s, --scope <SCOPE> Config scope: project or user [default: project].
• astra chat loads both project and user config: manifest_loader::collect_mcp_server_configs collects project .astra/mcp.json → skill manifests → ~/.astra/mcp.json (see crates/astra-cli/src/manifest_loader.rs).
• So a user-level-only setup is invisible to the default CLI listing, and no merged/effective view exists.
• crates/astra-cli/src/cli/mcp_config.rs (mcp_json_path_for_scope) resolves project vs user paths, but each listing command only shows one scope at a time.

Impact

Users following the user-level ~/.astra/mcp.json configuration path (which astra chat honors) get a misleading "No MCP servers configured" from astra mcp list, and cannot inspect the effective MCP setup without knowing to pass -s user. This makes debugging MCP configs confusing.

Related

• astra chat does not offer configured MCP tools to the model (servers connect but mcp__* tools absent from session tool pool) #621 — astra chat does not offer configured MCP tools to the model (the connected servers' tools are absent from the session tool pool).