Amazon Q CLI not loading MCP servers despite correct configuration

Can't use MCP anymore.

---
/tools

Tool Permission
---
Built-in:
- execute_bash * trust read-only commands
- fs_read * trusted
- fs_write * not trusted
- introspect * trusted
- report_issue * trusted
- use_aws * trust read-only commands

Servers still loading
---

- youtrack
- github
- todoist

---

#q diagnostic

[q-details]
version = "1.15.0"
hash = "eb8db5c635fc469f3bd94ead16bb4bfb32d7443b"
date = "2025-09-02T17:57:24.662205Z (1d ago)"
variant = "full"

[system-info]
os = "macOS 15.6.1 (24G90)"
chip = "Intel(R) Core(TM) i7-8850H CPU @ 2.60GHz"
total-cores = 6
memory = "16.00 GB"

[environment]
cwd = "/Users/USER"
cli-path = "/Users/USER"
os = "Mac"
shell-path = "/bin/zsh"
shell-version = "5.9"
terminal = "macOS"
install-method = "brew"

[env-vars]
PATH = "..........."
QTERM_SESSION_ID = "7e060ad9690b49b9935e7d13037e3182"
Q_SET_PARENT_CHECK = "1"
Q_TERM = "1.15.0"
SHELL = "/bin/zsh"
TERM = "xterm-256color"
__CFBundleIdentifier = "com.apple.Terminal"

---

# q doctor

✔ Everything looks good!

---

### **System Environment:**
• **Amazon Q CLI**: v1.15.0
• **OS**: Darwin 24.6.0 (macOS)
• **Node.js**: v24.7.0
• **NPM**: 11.5.1

### **MCP Configuration Status:**
✅ Configuration Files Present:
• ~/.aws/amazonq/mcp-servers.json (563 bytes)
• ~/.aws/amazonq/mcp.json → symlink to mcp-servers.json
• ~/.aws/amazonq/mcpAdmin/mcp-state.json → {"enabled":true}

✅ JSON Syntax: Valid JSON configuration

✅ MCP Servers Installed:
• @0xshariq/github-mcp-server@2.3.0
• youtrack-mcp-tonyzorin@1.17.3
• todoist-mcp@1.2.4

✅ Executables Present:
• GitHub: /usr/local/lib/node_modules/@0xshariq/github-mcp-server/start-mcp.sh
• YouTrack: /usr/local/bin/youtrack-mcp-tonyzorin
• Todoist: /usr/local/bin/todoist-mcp

✅ Environment Variables Set:
• GITHUB_TOKEN: SET (40 chars)
• YOUTRACK_TOKEN: SET (53 chars)
• TODOIST_API_TOKEN: SET (40 chars)

✅ Direct Server Tests:
• GitHub MCP: Responds to commands
• YouTrack MCP: v1.17.3 confirmed
• Todoist MCP: Executable (config issue noted)

### **Issues Identified:**
❌ No MCP Processes Running: No background MCP processes detected
❌ No MCP Settings: q settings shows no MCP-related configuration
❌ MCP Tools Not Loading: Despite perfect setup, no MCP tools available in Amazon Q CLI

### **Configuration Format Used:**
```json
{
"mcpServers": {
"github": {
"command": "npx",
"args": ["@0xshariq/github-mcp-server"],
"env": {"GITHUB_TOKEN": "${GITHUB_TOKEN}"}
}
}
}
```
---
Conclusion: All MCP components properly installed and configured, but Amazon Q CLI MCP system not initializing or loading servers.

---

## **MCP Log Analysis:**

### **Log File Locations:**
✅ Found: $TMPDIR/qlog/ directory with Amazon Q CLI logs
• **MCP Log**: /var/folders/.../qlog/mcp.log (0 bytes - empty)
• **Chat Log**: /var/folders/.../qlog/qchat.log (contains MCP errors)

### **Critical MCP Errors Found:**

1. Configuration Loading Errors:
Error loading global mcp json path: No such file or directory (os error 2). Skipping
Error loading global mcp json path: No mcp servers found in config. Skipping

2. MCP Client Connection Errors:
Error encountered while reading from stderr for github: RecvError(Closed)
Error encountered while reading from stderr for youtrack: RecvError(Closed)
Error encountered while reading from stderr for todoist: RecvError(Closed)

### **Root Cause Identified:**
❌ Amazon Q CLI is trying to load MCP servers but they're immediately closing/crashing
❌ MCP servers start but their stderr streams close immediately (RecvError(Closed))
❌ Configuration loading issues with "global mcp json path"

### **Key Evidence for GitHub Issue:**
• **MCP servers are being detected and started** by Amazon Q CLI
• **All three servers (github, youtrack, todoist) are failing with identical stderr errors**
• **MCP processes close immediately after starting**
• **Empty mcp.log indicates no successful MCP communication**

This log data proves Amazon Q CLI is attempting to load MCP servers but they're failing during initialization/communication phase.