feat(tools): Add `run_command` tool for the agentic loop

[sunilp]

Summary

Add a run_command tool that allows the model to execute shell commands in the jam run agentic loop.

Details

The file src/tools/run_command.ts already exists but may need to be registered and integrated into the tool registry.

Requirements

• Ensure run_command tool is properly implemented and registered
• Must be a write tool (requires user confirmation before execution)
• Should have safety guards: no rm -rf, no sudo, configurable via allowlist
• Capture stdout and stderr, return to the model
• Timeout after configurable duration (default: 30s)

Safety Considerations

• This is the highest-risk tool — confirmation prompt must clearly show the command
• Consider a separate dangerousCommandPatterns config option

Acceptance Criteria

• Tool registered in the registry
• User confirmation before every execution
• stdout/stderr captured and returned
• Timeout support
• Unit tests with mocked commands

[sunilp]

✅ Implemented and verified — closing

Merged in #11 (commit 1c908d9).

Delivered (changes to src/tools/run_command.ts + related files):

• runCommandTool export — a full ToolDefinition with readonly: false
• runCommand() return type changed from Promise<string> → Promise<{ stdout, stderr }> (all callers updated: git_diff.ts, git_status.ts, apply_patch.ts)
• Safety guards — DANGEROUS_PATTERNS regex list blocks: rm -rf, sudo, su -, mkfs, dd of=/dev/, block-device overwrites, chmod 777 /, shutdown, reboot
• stdout and stderr both captured and returned to the model ([stderr]\n... prefix)
• Configurable timeout (default 30s, accepts timeout arg in seconds)
• Registered in src/tools/registry.ts (write tool — always subject to policy confirmation)
• Schema also added to src/tools/all-tools.ts for jam run - Schema also added to src/tools/all-tools.ts for jam run - Schema also added to src/tools/all-tools.ts for jam run - ite- Schema also added to src/tools st- Schema also added to src/tools/all-tools.tsforjam run- Schpu- Schema also added tosrc/tools/all-tools.tsforjam run- Schema alommand- Schema also added tosrc/tools/all-tools.tsforjam run- Schema also added tosrc/tools/all-tools.tsforjam run- Schema also added tosrc/tools/all-toolsd produces no output
  passes timeout argument (uses seconds)