MCP tool schemas loaded from permissions even when server is not configured or removed

Description

MCP tool permissions stored in ~/.claude/settings.json and ~/.claude/settings.local.json cause tool schemas to be loaded into the prompt context even when the corresponding MCP server is no longer configured or has been completely removed.

Environment

• OS: macOS
• Claude Code: Latest CLI version

Observed Behavior

1. User configured desktop-commander MCP server in Project A
2. Used tools from that server, adding mcp__desktop-commander__* entries to permissions.allow
3. Later removed the server configuration from .claude.json
4. In a fresh session in a different project (Project B), Claude still had access to desktop-commander tool schemas
5. /mcp command shows no desktop-commander server configured
6. Yet the model's context included full tool definitions (~1-2k tokens)
7. After manually removing the orphaned mcp__desktop-commander__* entries from settings files, the tools disappeared from the model's context

Expected Behavior

• Tool schemas should only load when the MCP server is actually configured and connected
• Permissions referencing non-existent MCP tools should be ignored during context building
• Disabled or removed servers should not have their tool schemas loaded into prompt

Impact

| Issue | Severity |
|-------|----------|
| Users pay token costs for unused tool definitions | Medium |
| Tools appear available but may fail when invoked | High |
| /mcp command shows different state than actual model context | Medium |

Reproduction Steps

1. Add an MCP server (e.g., desktop-commander) to a project
2. Use tools from it so they get added to permissions.allow in ~/.claude/settings.json
3. Remove the server configuration from .claude.json
4. Start a fresh Claude Code session (different project or same project)
5. Run /mcp to confirm the server is not listed
6. Ask the model: "Do you have tools for desktop-commander?"
7. Observe that the model still believes it has access to the removed server's tools
8. Manually remove mcp__desktop-commander__* entries from settings files
9. Start fresh session - tools are now gone

Suggested Fix

1. Schema loading gate: Before loading tool schemas, verify the corresponding MCP server is currently configured and connected
2. Permission validation: Cross-reference permissions.allow entries with currently available MCP servers and skip loading schemas for non-existent tools
3. Optional cleanup: Consider a command like claude mcp prune that removes orphaned permission entries