Sub-agents spawned via Agent tool don't reliably inherit MCP tools (inconsistent with docs)

Summary

Sub-agents spawned directly via the Agent tool do not receive MCP tool access, even though the documentation states that sub-agents inherit all tools from the parent session (including MCP tools) by default.

Environment

• Claude Code version: latest (claude-sonnet-4-6)
• Platform: macOS Darwin 25.3.0
• MCP server: Atlassian (Jira)

Observed Behavior

Sub-agents spawned within a skill's execution context → ✅ MCP tools available (e.g. jira_get_issue, jira_search_fields, jira_create_issue — 17 successful MCP calls made)

Sub-agents spawned directly via the Agent tool (outside a skill context) → ❌ MCP tools not available. The agent reports only standard tools (Bash, Glob, Grep, Read, Edit, Write, etc.) and has no Jira/Atlassian tools in its tool list.

Reproduction Steps

1. Configure an Atlassian MCP server in Claude Code (~/.claude/settings.json)
2. Verify MCP is working (e.g. via a skill that uses Jira tools successfully)
3. Directly spawn a general-purpose sub-agent via the Agent tool:

``
Agent tool:
subagent_type: general-purpose
prompt: "Call jira_get_issue with issue_key 'PROJ-123' and return the result"
``

1. Observe that the sub-agent reports no MCP tools in its available tool list and cannot make the call

Expected Behavior

Per the documentation:

Subagents can use any of Claude Code's internal tools. By default, subagents inherit all tools from the main conversation, including MCP tools.

Sub-agents spawned via the Agent tool should have access to the same MCP tools available in the parent session, regardless of whether they are invoked within a skill context or directly.

Additional Context

The inconsistency is specifically between:

• Skill-invoked agents → MCP tools ✅
• Directly spawned agents (via Agent tool in main conversation) → MCP tools ❌

This suggests the skill execution framework passes MCP context through correctly, but the direct Agent tool invocation does not.