Extensions (e.g. Conductor) fail with "run_shell_command not found" + ask_user header >12 chars error + tool execution denied

[Wolfe-Jam]

Description

After successfully installing the Conductor extension (gemini extensions install https://github.com/gemini-cli-extensions/conductor --auto-update), commands like /conductor:setup fail with the following errors:

• Tool "run_shell_command" not found in registry
• params/questions/0/header must NOT have more than 12 characters (during interactive prompts)
• Tool execution denied by policy (occasional)

This prevents the interactive setup from completing (scaffolding conductor/ dir with product.md, plan.md, spec.md, etc.), making the extension's workflow inaccessible.

Environment

• Gemini CLI Version: 0.28.2 (Git Commit: da5e47a)
• Model: auto-gemini-2.5
• OS: darwin (macOS)
• Auth: Google login
• Sandbox: none
• Extension: Conductor (latest, including Automated Reviews)

Steps to Reproduce

1. Install Conductor extension as above.
2. cd into a project directory.
3. Run /conductor:setup.
   → Errors occur immediately or during prompt phase (full transcript in attachments).

Expected Behavior

Interactive setup completes, creating persistent Markdown files and enabling /conductor:review, etc.

Actual Behavior

Setup aborts due to tool/registry issues.

Additional Context

• Similar run_shell_command registry failures reported in other issues (Impossible to use Gemini for automation non-interactively #5382, The run_shell_command tool consistently fails with the error tool.startsWith is not a function. #7513, run_shell_command tool failure #13502).
• ask_user header limit appears resolved in preview releases (bumped to 16 chars in v0.29.0-preview).
• Tried: full folder trust, --yolo, --approval-mode auto_edit, CLI restart—no change.
• Minimal test extension also fails on run_shell_command → seems CLI-wide.

Attachments

• Session transcript (paste relevant parts here or attach bug-report.md).
• bug-report.md (your generated summary).

Suggestions

• Ensure run_shell_command is reliably available in extension contexts.
• Relax or increase ask_user header limit in stable release.
• Add clearer docs on enabling shell tools for extensions.

Appreciate the work on Gemini CLI and extensions—Conductor looks very promising for context-driven dev once these are sorted. Happy to test fixes or provide more logs.

Thanks!