fix: exempt shell tool from permission gating in buildToolConfig

[avoidwork]

Description

The shell tool was being gated by sandbox permissions in buildToolConfig, even though the permissions are already enabled in config. This caused the coding sub agent to see execute (from deepagents middleware) but not shell (the project's shell tool), leading to the error:

shell is not a valid tool, try one of [write_todos, ls, read_file, write_file, edit_file, glob, grep, execute]

Adding shell to the exempt case alongside clarify, executeCode, and sampling ensures it's always registered.

Type of Change

• Bugfix (non-breaking change which fixes an issue)
• New feature (non-breaking change which adds functionality)
• Breaking change (fix or feature that would cause existing functionality to not work as expected)
• Documentation update
• Refactor (no functional changes)
• Performance improvement
• CI / build / tooling

Testing

Unit test updated to expect 10 tools instead of 9 with filesystem:read permission.

Coverage

• Line coverage maintained

Checklist

• npm run lint passes
• Tests pass with maintained line coverage
• No forbidden patterns used
• Conventional Commit style applied

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Details

Commit(s): f8bb385 fix: exempt shell tool from permission gating in buildToolConfig

Changed files: src/tools/index.js, tests/unit/tool_index.test.js

Rule 5.4: PR template at .github/PULL_REQUEST_TEMPLATE.md was used. All sections filled.