feat: move SkillsMiddleware to core deepagents package (Issues: #506)

[Yo-sure]

Summary

Closes #506

Moves SkillsMiddleware from deepagents-cli to the core deepagents package.
This improves code reusability and allows the Skills system to be used in various environments.

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Changes

File	Change
deepagents/middleware/skills.py	✨ New file - logic moved from CLI
deepagents/middleware/__init__.py	Added SkillsMiddleware export
deepagents-cli/skills/*.py	Re-export from core (backward compatibility)
tests/unit_tests/test_middleware.py	Added 17 tests

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Usage

from deepagents.middleware import SkillsMiddleware

agent = create_deep_agent(
    model=model,
    middleware=[
        SkillsMiddleware(
            skills_dir="~/.myapp/skills",
            assistant_id="my-agent",
            project_skills_dir="./.skills",  # optional
        )
    ],
)

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Design Decisions

Export Scope

• deepagents/__init__.py: No changes
• deepagents.middleware: Only SkillsMiddleware exposed
• deepagents.middleware.skills: Full API (list_skills, SkillMetadata, etc.)

Backward Compatibility

All existing CLI import paths and behaviors are preserved:

from deepagents_cli.skills import SkillsMiddleware  # Still works (re-export)

• CLI usage: Existing paths (~/.deepagents/{AGENT_NAME}/skills/) unchanged
• Core direct usage: Paths can be freely specified

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Testing

Unit Tests

• Core Skills tests: 17 added (78 total passed)
• CLI Skills tests: 25 passed

pytest tests/unit_tests/test_middleware.py  # 78 passed

Integration Tests (Actual Operation Verified)

• ✅ Core: DeepAgent + SkillsMiddleware + LLM call
• ✅ Core: User skills + Project skills + Override behavior
• ✅ CLI: deepagents skills list (User + Project)
• ✅ CLI: Actual LLM call (User + Project skills recognized)

NO CLI (Core)

CLI

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Checklist

• References Issue Add option to use skills in custom agent base on deepagents (non-cli version) #506
• Branch naming convention (Yo-sure/add-skills-to-core)
• Tests written and passing
• lint/format passing
• Backward compatibility maintained
• Minimal change principle
• Actual operation verified (Core + CLI)