Tool execution delay and intermittent timeouts despite fast actual command execution

Description

Experiencing frequent tool execution delays and intermittent timeouts when using Bash tool with SSH/MySQL commands, even though the actual command execution is very fast.

Environment

• Claude Code version: Latest
• OS: Linux (Synology NAS via SSH)
• Connection: Local SSH to NAS server

Steps to Reproduce

1. Execute SSH command to remote MySQL database
2. Run queries on a table with ~5,500 rows
3. Observe delays or timeouts despite fast query execution

Evidence

SSH connection test:

real    0m0.169s
user    0m0.018s
sys     0m0.004s

MySQL query execution time:

• Start: 2026-02-06 10:48:48.860
• End: 2026-02-06 10:48:48.918
• Actual execution: 0.058 seconds

Despite the query completing in ~60ms, the tool call sometimes:

• Takes several seconds to return
• Times out completely
• Gets interrupted

Expected Behavior

Tool calls should return promptly when the underlying command completes quickly.

Actual Behavior

• Intermittent delays (several seconds) even for fast commands
• Occasional timeouts despite successful command execution
• User experience degraded due to unpredictable response times

Frequency

This occurs frequently (not occasionally), making it a significant usability issue.

Additional Context

• Database has proper indexes (name, phone, address all indexed)
• Network latency is minimal (0.17s SSH connection)
• Issue appears to be in Claude Code infrastructure, not in the actual command execution