Add MCP permission docs and shell script linting rules

[ydesgagn]

Summary

Add documentation for recommended MCP server permissions and extend the run-linters skill with shell script linting guidance.

Key changes:

• Add "Recommended Permissions" section to README.md with permissions.allow patterns for bundled and remote MCP servers
• Add shell script linting rules (SL0001, SL0002) to the run-linters skill covering brace-wrapped variables and == for string comparison
• Add general shell script best practices (quoting, [[ over [, $(command) over backticks)

Types of changes

• Bugfix (fixes an issue)
• New feature (adds functionality)
• Refactoring (improves code without changing functionality)
• Breaking change (incompatible changes)
• Build or security update (updates dependencies, libraries, or security patches)
• Code style or documentation update (formatting, renaming, or documentation changes)
• Other (please describe):

Checklist

• Unit tests added to validate my fix/feature
• I have manually tested my change
• I did not add automation test. Why ?: Documentation and skill definition changes only
• Database changes requiring migration with downtime or reprocessing of existing data
• The SOUP file lists the risk Level, requirements and verification reasoning associated with each library
• readme.md includes sections on introduction, installation, usage, and contributing
• docs/architecture.md includes sections on the architecture diagram, software units, software of unknown provenance, critical algorithms and risk controls related to PII and security
• Impact on PII, privacy regulations (CCPA/GDPR/PIPEDA), CIS benchmarks or security (availability/confidentiality/integrity); management must be notified