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Add a CLI flag to configure MCP roots #2598

Description

@OrKoN

Is your feature request related to a problem? Please describe.

Currently, the file system access can only be configured via MCP. In the next version of the MCP spec, the roots are getting removed.

Describe the solution you'd like

We should also support a CLI flag like --filesystem-root (array) and via --workspace (array) keeping the defaults to the os.tmpdir().

Describe alternatives you've considered

Removing roots altogether, discarded since it's useful to set fs guardrails for the mcp server and cli.

Additional context

No response

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