fix: resolve tool duplication and skill parser YAML inconsistencies (#1803)

[asong56]

Description

This PR addresses two root causes of systematic tool failure (name duplication):

1. Deduplication in get_available_tools: Added a "first-occurrence-wins" deduplication step to prevent the LLM from receiving multiple schemas for the same tool (which caused name concatenation like lsls).
2. YAML Parser Inconsistency: Replaced a custom line-by-line parser in skills/parser.py with yaml.safe_load. The previous custom parser incorrectly handled quoted strings and ignored list values, leading to registration mismatches.

Additionally, added a warning for cases where a tool's config name differs from its decorated .name attribute.

Changes

• Modified backend/packages/harness/deerflow/tools/tools.py
• Modified backend/packages/harness/deerflow/skills/parser.py
• Added backend/tests/test_skills_parser_issue1803.py
• Added backend/tests/test_tools_deduplication_issue1803.py

Checklist

• Verified backward compatibility with existing SKILL.md files.
• Added regression tests for YAML quoting and tool deduplication.

closes #1803

[Copilot]

Pull request overview

This PR fixes two root causes behind systematic tool invocation failures in DeerFlow: duplicate tool registrations (leading to ambiguous tool schemas) and inconsistent YAML parsing between SKILL.md parsing vs validation.

Changes:

• Added name-based, first-occurrence-wins deduplication to get_available_tools(), with warnings for duplicates and for config-name vs tool-name mismatches.
• Replaced the hand-rolled SKILL.md front-matter parser with yaml.safe_load for consistent YAML semantics (quoting, multiline, etc.).
• Added/updated regression tests covering tool deduplication and YAML front-matter parsing edge cases.

Reviewed changes

Copilot reviewed 4 out of 4 changed files in this pull request and generated 4 comments.

File	Description
backend/packages/harness/deerflow/tools/tools.py	Adds tool-name mismatch warning + name-based deduplication of the final tool list returned to the agent/runtime.
backend/packages/harness/deerflow/skills/parser.py	Switches SKILL.md front-matter parsing to yaml.safe_load and tightens type/emptiness checks for required fields.
backend/tests/test_tool_deduplication.py	New regression tests to ensure get_available_tools() never returns duplicate tool names and logs warnings on duplicates.
backend/tests/test_skills_parser.py	Updates tests to specifically cover the quoted-string YAML regression and related parser behaviors.

Comments suppressed due to low confidence (1)

backend/packages/harness/deerflow/tools/tools.py:87

• The conditional inclusion of skill_manage_tool when config.skill_evolution.enabled is true was removed. If skill self-evolution is still supported, this change likely prevents the agent from ever being able to create/patch skills via the skill_manage tool unless users manually add it to config.tools. Please either restore the conditional append (or otherwise ensure skill_manage_tool is exposed when skill evolution is enabled) and add a regression test around get_available_tools() for this behavior.

    # Conditionally add tools based on config
    builtin_tools = BUILTIN_TOOLS.copy()

    # Add subagent tools only if enabled via runtime parameter
    if subagent_enabled:
        builtin_tools.extend(SUBAGENT_TOOLS)
        logger.info("Including subagent tools (task)")

[asong56]

changed test_tool_deduplication.py and test_skills_parser.py

[WillemJiang]

@asong56

skill_manage_tool silently removed (tools.py:64-70 diff)

The PR deletes the conditional inclusion of skill_manage_tool:

  # REMOVED by this PR:
  skill_evolution_config = getattr(config, "skill_evolution", None)
  if getattr(skill_evolution_config, "enabled", False):
      from deerflow.tools.skill_manage_tool import skill_manage_tool
      builtin_tools.append(skill_manage_tool)

This means skill self-evolution (the ability for the agent to create/patch skills via the skill_manage tool) is completely broken when skill_evolution.enabled = true in config. The tool simply won't appear in the agent's toolset.

Fix: Restore the conditional block. It should come after the BUILTIN_TOOLS.copy() line and before the deduplication logic.

[asong56]

added back

[WillemJiang]

added back

@asong56, I checked the change. Please keep the comments on the code and fix the lint error.

[asong56]

done

[WillemJiang]

@asong56, please use the command to fix the lint error

cd backend
make format

[asong56]

Done