fix: remove misleading @defer decorator comments

[MarioAderman]

Description

Removes all misleading references to non-existent @defer decorator from the codebase. Neither pydantic_ai nor pydantic_graph uses the so-called decorator. For simplicity's sake references were removed.

Type of Change

• 🐛 Bug fix (non-breaking change which fixes an issue)
• 📚 Documentation update

Component

• Tool Registry
• Bioinformatics Flow (Data Fusion)
• Agent System
• Documentation

Related Issues

• Fixes [BUG]: Pydantic-AI defer decorator not available in current version #2

Changes Made

• Removed 7 misleading @defer comments from DeepResearch/src/tools/deep_agent_tools.py
• Removed 10 misleading @defer comments from DeepResearch/src/tools/bioinformatics_tools.py
• Removed misleading "Register Deferred Tools" code example section from README.md

Testing

• I have tested these changes locally
• All existing tests pass
• I have tested with different configurations

Test Configuration

# No functional changes - only documentation/comments removed
# All tools continue to work correctly with standard Pydantic AI patterns
uv run pytest tests/ -v

Configuration Changes

• No configuration changes

Documentation

• Updated README
• Added code comments

Performance Impact

• No performance impact

Zero functional changes - only misleading documentation removed.

Breaking Changes

• No breaking changes

Checklist

• My code follows the project's style guidelines
• I have performed a self-review of my own code
• I have commented my code, particularly in hard-to-understand areas
• I have made corresponding changes to the documentation
• My changes generate no new warnings
• New and existing unit tests pass locally with my changes
• Any dependent changes have been merged and published

Additional Notes

Investigation Summary

Key Finding: The @defer decorator NEVER existed in Pydantic AI (verified across all versions).

Screenshots/Output

Before

# Note: defer decorator is not available in current pydantic-ai version

# @defer - not available in current pydantic-ai version
def write_todos_tool(request: WriteTodosRequest, ctx: RunContext[DeepAgentState]):
    ...

After

def write_todos_tool(request: WriteTodosRequest, ctx: RunContext[DeepAgentState]):
    ...

Reviewer Notes

This PR only removes misleading documentation. No functional code changes were made. All tools continue to work correctly as they were already implemented using proper Pydantic AI patterns.

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.

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