Custom agent with tools specification (run as subagent) confuses them with lack of skills

### Describe the bug

_No response_

### Affected version

_No response_

### Steps to reproduce the behavior

- Have a custom agent X with tools specification and in instructions point to using some skills
- Run the agent as the subagent of e.g. orchestrator agent
- Observe the the custom agent X confuses tools with skills and reports lack of skills available

### Expected behavior

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### Additional context

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Start by reproducing the custom agent X scenario described in the issue: give it a tools specification, reference skills in its instructions, and run it as a subagent of an orchestrator agent. Compare how the subagent interprets tools and skills; done means it no longer reports that referenced skills are unavailable when tools were specified.

Written by the indexing model from the issue text.