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Add deprecation notices for legacy agent skills #6511

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This PR adds deprecation notices and migration documentation for legacy agent skills as part of issue #6083.

Changes

  1. Added comprehensive migration guide from agent skills to function calls
  2. Added deprecation warnings to:
    • Main agent_skills module
    • file_ops module
    • file_reader module
  3. Updated configuration documentation with deprecation notice
  4. Set clear timeline for removal in v0.22.0

Migration Timeline

  • v0.21.0: Add deprecation notices (this PR)
  • v0.22.0: Remove legacy agent skills

Testing

  • Verify deprecation warnings appear when using legacy agent skills
  • Verify documentation links work correctly
  • Verify configuration documentation is accurate

Fixes #6083

- Add migration guide from agent skills to function calls
- Add deprecation warnings to agent skills modules
- Update configuration documentation with deprecation notice
- Document timeline for removal in v0.22.0
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Successfully merging this pull request may close these issues.

Clean up unused agent skills after function calling migration
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