Move permissions documentation to reference section after CLI

[Copilot]

Overview

This PR reorganizes the documentation structure by moving the permissions guide from the "Using Wassette" section to the "Reference" section, positioning it immediately after the CLI reference documentation.

Changes

Documentation Structure

• Moved docs/using/permissions.md → docs/reference/permissions.md
• Updated docs/SUMMARY.md to reflect the new location
• Removed the now-empty "Using Wassette" section from the table of contents
• The Reference section now contains both CLI and Permissions documentation:

  # Reference
  - [CLI](./reference/cli.md)
  - [Permissions](./reference/permissions.md)

Internal Link Updates

• Updated relative link in permissions.md: ../reference/cli.md → ./cli.md (now in same directory)
• Other relative links remain correct (../faq.md, ../design/permission-system.md)

Rationale

This change improves documentation organization by:

• Grouping reference materials together: Both CLI commands and permissions management are reference-style documentation that users look up when needed
• Better discoverability: Users looking for CLI reference information will now find permissions documentation in the same section
• Cleaner structure: The "Using Wassette" section can be reserved for future practical how-to guides and tutorials

Verification

The documentation structure has been validated:

• File successfully moved with git history preserved
• Table of contents correctly updated
• Internal links verified and corrected where needed
• CI will validate the mdbook build on this PR

Original prompt

Move the permissions document to reference section, after cli.md

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